Purification, SDS-PAGE and cryo-em characterization of the MCM hexamer and Cdt1 MCM heptamer samples.
|
|
|
- Roxanne Burke
- 5 years ago
- Views:
Transcription
1 Supplementary Figure 1 Purification, SDS-PAGE and cryo-em characterization of the MCM hexamer and Cdt1 MCM heptamer samples. (a-b) SDS-PAGE analysis of the hexamer and heptamer samples. The eluted hexamer (a) and heptamer (b) complexes were subjected to 20 40% glycerol gradient sedimentation centrifugation. Collected fractions were analyzed by SDS-PAGE and visualized by coomassie blue staining. Molecular size markers used are: ALP 140 kda and thyroglobulin 669 kda. Fractions 7-9 (a) and 8-10 (b) were pooled and concentrated for cryo-em analysis. (c) The sedimentation profile of Mcm5 and Cdt1 from the hexamer (a) and heptamer (b) samples were plotted using quantified signals by Image J. (d) A representative raw micrograph of Cdt1 Mcm2-7 complexes in vitreous ice. (e-g) Representative 2D class averages of cryo-em particles from the datasets of heptamer+amppnp (e), heptamer+adp (f), and hexamer+adp+np40 (g). See also Table 1.
2
3 Supplementary Figure 2 Flowchart for image processing of particles from the heptamer + AMPPNP data set and Fourier shell correlation curves of the five structures. (a) A flowchart of the steps in image processing. (b-f), Fourier Shell Correlation curves of the heptamer AMPPNP (b), heptamer ADP (c), hexamer AMPPNP (d), hexamer ADP (e) and (hexamer ADP)* (f) structures. Note that (hexamer ADP)* is the hexamer structure from the dataset of heptamer + ADP. See also Table 1.
4 Supplementary Figure 3 Overall structures of the heptamer and hexamer. (a-c) Top panels, The cryo-em maps of the indicated complexes are shown in surface representation, with individual components color coded. Bottom panel, the maps are shown in transparent surface representation, with models superimposed. Both the CTD top-view
5 and consecutively rotated side-views are shown. a, hexamer AMPPNP. b, heptamer ADP c, hexamer ADP.
6 Supplementary Figure 4 Arrangements of oligonucleic-acid-binding subdomains (OBs) in the heptamer and double hexamer. (a-b) Arrangements of OB subdomains from the heptamer (a), and the double hexamer (b). Models are shown in ribbon representation. Individual OB subdomains are color-coded. (c-d) Superimposition of OB subdomains from heptamer (color-coded) and double hexamer (grey), shown in top (c) and side (d) views. The alignment is done using the OB of Mcm7 as reference.
7 Supplementary Figure 5 Constellation of Cdt1-binding sites in the heptamer and double hexamer. (a) The binding sites of Cdt1 on the NTD of Mcm2 (orange), CTD-A of Mcm6 (blue) and NTD of Mcm4 (magenta) as well as the two interacting N-C-linkers of Mcm6 (sky blue) and Mcm4 (red) in the heptamer are highlighted in different colors. (b) The MCM single hexamer from the double hexamer is aligned to the heptamer and shown in a similar orientation as in (a), with Cdt1 binding sites mapped. The NTD of Mcm6 (tan) is used as reference for the alignment.
8 Supplementary Figure 6 Structural comparison of the heptamer and double hexamer. (a-f) Conformational differences of each NTDs from the heptamer and the double hexamer. NTD-A was used as reference for the alignment. NTDs of the heptamer are color coded and the corresponding NTDs in the DH are in grey. Dramatic changes are observed for the ZF motifs of Mcm2 (20 Å) and Mcm3 (10 Å). The distance changes of the other motifs of NTDs (ZF and OB) are measured by r.m.s.d. (root-mean-square deviation). r.m.s.d. values: M2 (7.5 Å), M6 (1.9 Å), M4 (2.0 Å), M7 (1.6 Å), M3 (3.5 Å), M5 (2.2 Å). (g-k) Conformational differences of the CTD-A dimers in the heptamer (color-coded for subunits) and in the double hexamer (grey). One CTD-A of each neighboring pairs (the left one) was used as the reference for alignment. Calculated r.m.s.d values of the other CTD-As are: M6 (4.3 Å), M4 (6.0 Å), M7 (6.8 Å), M3 (6.1 Å), M5 (5.0 Å).
9 Supplementary Figure 7 Cdc45 and GINS are structurally incompatible for interactions with MCM subunits in the heptamer and open- and closed-ring conformations of different MCM complexes. (a) Structure of the CMG complex in surface representation. The map of the CMG was converted from a previous atomic model (PDB 3JC5). Mcm5, Mcm2, GINS, Cdc45 are colored yellow, orange, sky blue and purple, respectively. (b) Structure of the Cdt1 Mcm2-7 heptamer, displayed in a comparable orientation as in (a). (c-d) Superimposition of Cdc45 and GINS from the CMG structure onto the map of the heptamer, showing in top (c) and side (d) views. Mcm2-NTD was used as reference for the alignment. As shown, aligned
10 Cdc45/GINS exhibits structural conflict with the CTD-A of Mcm5 in the heptamer, indicating that the interactions of Cdc45/GINS with the NTDs of Mcm5 and Mcm2 observed in the CMG complex could not be simultaneously satisfied in the heptamer. (e) CTD top views of the cryo-em maps (grey) of the yeast MCM hexamer, Cdt1 MCM heptamer, and double hexamer (EMD-6338). The double hexamer map is low-pass filter to 10 Å. (f) CTD top views of the two conformers of the yeast CMG complex (EMD-6536 and EMD-6535). (g) CTD top views of the two conformers of the Drosophila CMG complex (EMD-3321 and EMD-3320).
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11991 Supplementary Figure 1 - Refinement strategy for PIC intermediate assemblies by negative stain EM. The cryo-negative stain structure of free Pol II 1 (a) was used as initial reference
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Identification of the ScDcp2 minimal region interacting with both ScDcp1 and the ScEdc3 LSm domain. Pull-down experiment of untagged ScEdc3 LSm with various ScDcp1-Dcp2-His 6 fragments.
SUPPLEMENTARY INFORMATION
Supplementary materials Figure S1 Fusion protein of Sulfolobus solfataricus SRP54 and a signal peptide. a, Expression vector for the fusion protein. The signal peptide of yeast dipeptidyl aminopeptidase
SUPPLEMENTARY INFORMATION
Supplementary Table 1: Amplitudes of three current levels. Level 0 (pa) Level 1 (pa) Level 2 (pa) TrkA- TrkH WT 200 K 0.01 ± 0.01 9.5 ± 0.01 18.7 ± 0.03 200 Na * 0.001 ± 0.01 3.9 ± 0.01 12.5 ± 0.03 200
SUPPLEMENTARY INFORMATION
SUPPLMTARY IFORMATIO a doi:10.108/nature10402 b 100 nm 100 nm c SAXS Model d ulers assigned to reference- Back-projected free class averages class averages Refinement against single particles Reconstructed
Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits. AhpC and AhpF from Escherichia coli
Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli Phat Vinh Dip 1,#, Neelagandan Kamariah 2,#, Malathy Sony Subramanian Manimekalai
of the Guanine Nucleotide Exchange Factor FARP2
Structure, Volume 21 Supplemental Information Structural Basis for Autoinhibition of the Guanine Nucleotide Exchange Factor FARP2 Xiaojing He, Yi-Chun Kuo, Tyler J. Rosche, and Xuewu Zhang Inventory of
Supplemental Figure and Movie Legends Figure S1. Time course experiments on the thermal stability of apo AT cpn-α by native PAGE (related to Figure 2B). The samples were heated, respectively, to (A) 45
Supplementary Figure 1. Biochemical and sequence alignment analyses the
Supplementary Figure 1. Biochemical and sequence alignment analyses the interaction of OPTN and TBK1. (a) Analytical gel filtration chromatography analysis of the interaction between TBK1 CTD and OPTN(1-119).
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the
SI Text S1 Solution Scattering Data Collection and Analysis. SI references
SI Text S1 Solution Scattering Data Collection and Analysis. The X-ray photon energy was set to 8 kev. The PILATUS hybrid pixel array detector (RIGAKU) was positioned at a distance of 606 mm from the sample.
Cryo-EM data collection, refinement and validation statistics
1 Table S1 Cryo-EM data collection, refinement and validation statistics Data collection and processing CPSF-160 WDR33 (EMDB-7114) (PDB 6BM0) CPSF-160 WDR33 (EMDB-7113) (PDB 6BLY) CPSF-160 WDR33 CPSF-30
Supplemental Data SUPPLEMENTAL FIGURES
Supplemental Data CRYSTAL STRUCTURE OF THE MG.ADP-INHIBITED STATE OF THE YEAST F 1 C 10 ATP SYNTHASE Alain Dautant*, Jean Velours and Marie-France Giraud* From Université Bordeaux 2, CNRS; Institut de
RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex
Molecular Cell, Volume 39 Supplemental Information RNA Polymerase I Contains a TFIIFRelated DNABinding Subcomplex Sebastian R. Geiger, Kristina Lorenzen, Amelie Schreieck, Patrizia Hanecker, Dirk Kostrewa,
Supplementary Materials for
advances.sciencemag.org/cgi/content/full/3/6/e1700147/dc1 Supplementary Materials for Ribosome rearrangements at the onset of translational bypassing Xabier Agirrezabala, Ekaterina Samatova, Mariia Klimova,
SUPPLEMENTARY INFORMATION
www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
SUPPLEMENTARY INFORMATION
doi:10.1038/nature10955 Supplementary Figures Supplementary Figure 1. Electron-density maps and crystallographic dimer structures of the motor domain. (a f) Stereo views of the final electron-density maps
Structural characterization of NiV N 0 P in solution and in crystal.
Supplementary Figure 1 Structural characterization of NiV N 0 P in solution and in crystal. (a) SAXS analysis of the N 32-383 0 -P 50 complex. The Guinier plot for complex concentrations of 0.55, 1.1,
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis Sergio de Cima, Luis M. Polo, Carmen Díez-Fernández, Ana I. Martínez, Javier
Three-dimensional structure of a viral genome-delivery portal vertex
Three-dimensional structure of a viral genome-delivery portal vertex Adam S. Olia 1, Peter E. Prevelige Jr. 2, John E. Johnson 3 and Gino Cingolani 4 1 Department of Biological Sciences, Purdue University,
Supplementary Figures
Supplementary Figures Supplementary Figure 1. Purification of yeast CKM. (a) Silver-stained SDS-PAGE analysis of CKM purified through a TAP-tag engineered into the Cdk8 C-terminus. (b) Kinase activity
Supplementary Information. The protease GtgE from Salmonella exclusively targets. inactive Rab GTPases
Supplementary Information The protease GtgE from Salmonella exclusively targets inactive Rab GTPases Table of Contents Supplementary Figures... 2 Supplementary Figure 1... 2 Supplementary Figure 2... 3
SUPPLEMENTARY INFORMATION
Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Cryo-EM structure and model of the C. thermophilum 90S preribosome. a, Gold standard FSC curve showing the average resolution of the 90S preribosome masked and unmasked (left). FSC
Supplemental Information. Expanded Coverage of the 26S Proteasome. Conformational Landscape Reveals. Mechanisms of Peptidase Gating
Cell Reports, Volume 24 Supplemental Information Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating Markus R. Eisele, Randi G. Reed, Till Rudack, Andreas
SUPPLEMENTARY INFORMATION
Fig. 1 Influences of crystal lattice contacts on Pol η structures. a. The dominant lattice contact between two hpol η molecules (silver and gold) in the type 1 crystals. b. A close-up view of the hydrophobic
Spliceosome and Localization of Its Catalytic Core
Molecular Cell, Volume 40 Supplemental Information 3D Cryo-EM Structure of an Active Step I Spliceosome and Localization of Its Catalytic Core Monika M. Golas, Bjoern Sander, Sergey Bessonov, Michael Grote,
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b).
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b). Crystal contacts at B-C loop are magnified and stereo view of A-weighted
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R)
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R) Shown in cyan and green are two adjacent tetramers from the crystallographic lattice of COP, forming the only unique inter-tetramer
SUPPLEMENTARY FIGURES. Figure S1
SUPPLEMENTARY FIGURES Figure S1 The substrate for DH domain (2R,3R,4R,6R,7S,8S,9R)-3,7,9-trihydroxy-5-oxo-2,4,6,8 tetramethylundecanoate) was docked as two separate fragments shown in magenta and blue
Supplementary Information
Supplementary Information The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis Marta C. Marques a, Cristina Tapia b, Oscar Gutiérrez-Sanz b, Ana Raquel Ramos a, Kimberly L.
SUPPLEMENTARY INFORMATION
doi:10.1038/nature12045 Supplementary Table 1 Data collection and refinement statistics. Native Pt-SAD X-ray source SSRF BL17U SPring-8 BL41XU Wavelength (Å) 0.97947 1.07171 Space group P2 1 2 1 2 1 P2
Supplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate
SUPPLEMENTARY FIGURE LEGENDS Supplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate dehydrogenase from Escherichia coli [ICD, pdb 1PB1, Mesecar, A. D., and Koshland,
V19 Topology of Protein Complexes on Graphs
V19 Topology of Protein Complexes on Graphs (1) CombDock (2) Nuclear Pore Complex 19. Lecture WS 2013/14 Bioinformatics III 1 Prediction Structures of Protein Complexes from Connectivities CombDock: automated
Supplementary Figure 1. SDS-PAGE analysis of GFP oligomer variants with different linkers. Oligomer mixtures were applied to a PAGE gel containing
Supplementary Figure 1. SDS-PAGE analysis of GFP oligomer variants with different linkers. Oligomer mixtures were applied to a PAGE gel containing 0.1% SDS without boiling. The gel was analyzed by a fluorescent
Supplementary Information
Supplementary Information Resveratrol Serves as a Protein-Substrate Interaction Stabilizer in Human SIRT1 Activation Xuben Hou,, David Rooklin, Hao Fang *,,, Yingkai Zhang Department of Medicinal Chemistry
Structure and RNA-binding properties. of the Not1 Not2 Not5 module of the yeast Ccr4 Not complex
Structure and RNA-binding properties of the Not1 Not2 Not5 module of the yeast Ccr4 Not complex Varun Bhaskar 1, Vladimir Roudko 2,3, Jerome Basquin 1, Kundan Sharma 4, Henning Urlaub 4, Bertrand Seraphin
Supplementary figure 1 Application of tmfret in LeuT. (a) To assess the feasibility of using tmfret for distance-dependent measurements in LeuT, a
Supplementary figure 1 Application of tmfret in LeuT. (a) To assess the feasibility of using tmfret for distance-dependent measurements in LeuT, a series of tmfret-pairs comprised of single cysteine mutants
Supplementary Figure 1
Supplementary Figure 1 The correlation of n-score cutoff and FDR in both CID-only and CID-ETD fragmentation strategies. A bar diagram of different n-score thresholds applied in the search, plotted against
Supplementary Figure 1A Supplementary Figure 1B
B A C Supplementary Figure 1A. (A) superposition of example decoy geometries as seen from the side and top. (B) docking of a section of the minimum stress decoy structure into the EMD-5136 electron density
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature12242 C. thermophilum 666 RPAVLDNVYIRPALE-GKRVPGKVEIHQNGIRYQSPLSTTQRVDVLFSNIRHLFFQPCQN S. pombe 659 RPAHINDVYVRPAID-GKRLPGFIEIHQNGIRYQSPLRSDSHIDLLFSNMKHLFFQPCEG
The Fic protein Doc uses an inverted substrate to phosphorylate and. inactivate EF-Tu
The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu Daniel Castro-Roa 1, Abel Garcia-Pino 2,3 *, Steven De Gieter 2,3, Nico A.J. van Nuland 2,3, Remy Loris 2,3, Nikolay
Structural insights into WcbI, a novel polysaccharide-biosynthesis enzyme
Volume 1 (2014) Supporting information for article: Structural insights into WcbI, a novel polysaccharide-biosynthesis enzyme Mirella Vivoli, Emily Ayres, Edward Beaumont, Michail N. Isupov and Nicholas
Supplementary Information: Long range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Supplementary Information: Long range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs
Supporting Information
Supporting Information Ottmann et al. 10.1073/pnas.0907587106 Fig. S1. Primary structure alignment of SBT3 with C5 peptidase from Streptococcus pyogenes. The Matchmaker tool in UCSF Chimera (http:// www.cgl.ucsf.edu/chimera)
THE CRYSTAL STRUCTURE OF THE SGT1-SKP1 COMPLEX: THE LINK BETWEEN
THE CRYSTAL STRUCTURE OF THE SGT1-SKP1 COMPLEX: THE LINK BETWEEN HSP90 AND BOTH SCF E3 UBIQUITIN LIGASES AND KINETOCHORES Oliver Willhoft, Richard Kerr, Dipali Patel, Wenjuan Zhang, Caezar Al-Jassar, Tina
SUPPLEMENTARY INFORMATION
Supplementary Table S1 Kinetic Analyses of the AMSH-LP mutants AMSH-LP K M (μm) k cat x 10-3 (s -1 ) WT 71.8 ± 6.3 860 ± 65.4 T353A 76.8 ± 11.7 46.3 ± 3.7 F355A 58.9 ± 10.4 5.33 ± 0.30 proximal S358A 75.1
SUPPLEMENTARY INFORMATION
Supplementary Table 1: Data collection, phasing and refinement statistics ChbC/Ta 6 Br 12 Native ChbC Data collection Space group P4 3 2 1 2 P4 3 2 1 2 Cell dimensions a, c (Å) 132.75, 453.57 132.81, 452.95
Supplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine
Supplementary figure 1. Comparison of unbound and as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine GM-CSF (slate) with bound GM-CSF in the GIF:GM-CSF complex (GIF: green,
SUPPLEMENTARY INFORMATION
doi:10.108/nature11899 Supplementar Table 1. Data collection and refinement statistics (+TPMP, native) (-TPMP, native) (+TPMP, recombinant) (MgCl ) (MgSO ) Data collection Space group C P 1 C P 1 1 P 1
Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1. Definition and assessment of ciap1 constructs.
Supplementary Figure 1 Definition and assessment of ciap1 constructs. (a) ciap1 constructs used in this study are shown as primary structure schematics with domains colored as in the main text. Mutations
Cks1 CDK1 CDK1 CDK1 CKS1. are ice- lobe. conserved. conserved
Cks1 d CKS1 Supplementary Figure 1 The -Cks1 crystal lattice. (a) Schematic of the - Cks1 crystal lattice. -Cks1 crystallizes in a lattice that contains c 4 copies of the t - Cks1 dimer in the crystallographic
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11744 Supplementary Table 1. Crystallographic data collection and refinement statistics. Wild-type Se-Met-BcsA-B SmCl 3 -soaked EMTS-soaked Data collection Space
SUPPLEMENTARY INFORMATION. doi: /nature07461
Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of
Supporting Online Material for
www.sciencemag.org/cgi/content/full/310/5753/1513/dc1 Supporting Online Material for Structural Roles for Human Translation Factor eif3 in Initiation of Protein Synthesis Bunpote Siridechadilok, Christopher
Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions. Implicated in Dimerization and Autoinhibition
JBC Papers in Press. Published on November 1, 2000 as Manuscript M006502200 Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions Implicated in Dimerization and Autoinhibition 1 Copyright
Time-dependence of key H-bond/electrostatic interaction distances in the sirna5-hago2 complexes... Page S14
Supporting Information Probing the Binding Interactions between Chemically Modified sirnas and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations S. Harikrishna* and P. I. Pradeepkumar*
Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet
SUPPLEMENTARY INFORMATION TO Structural basis for enzymatic excision of N -methyladenine and N 3 -methylcytosine from DNA Ingar Leiros,5, Marivi P. Nabong 2,3,5, Kristin Grøsvik 3, Jeanette Ringvoll 2,
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
Stabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon
Stabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon Wentao Chen,, Leopold Kong, Stephen Connelly, Julia M. Dendle,, Yu Liu,, Ian A. Wilson,#, Evan T. Powers, *, Jeffery
ICM-Chemist-Pro How-To Guide. Version 3.6-1h Last Updated 12/29/2009
ICM-Chemist-Pro How-To Guide Version 3.6-1h Last Updated 12/29/2009 ICM-Chemist-Pro ICM 3D LIGAND EDITOR: SETUP 1. Read in a ligand molecule or PDB file. How to setup the ligand in the ICM 3D Ligand Editor.
Supplementary Figures
1 Supplementary Figures Supplementary Figure 1 Type I FGFR1 inhibitors (a) Chemical structures of a pyrazolylaminopyrimidine inhibitor (henceforth referred to as PAPI; PDB-code of the FGFR1-PAPI complex:
Supplemental Information. The Mitochondrial Fission Receptor MiD51. Requires ADP as a Cofactor
Structure, Volume 22 Supplemental Information The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor Oliver C. Losón, Raymond Liu, Michael E. Rome, Shuxia Meng, Jens T. Kaiser, Shu-ou Shan,
SUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background.
SUPPLEMENTARY INFORMATION
doi:10.1038/nature10162 Architecture of the Mediator Head module Tsuyoshi Imasaki, Guillermo Calero, Gang Cai, Kuang-Lei Tsai, Kentaro Yamada, Francesco Cardelli, Hediye Erdjument-Bromage, Paul Tempst,
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Crystallization. a, Crystallization constructs of the ET B receptor are shown, with all of the modifications to the human wild-type the ET B receptor indicated. Residues interacting
SUPPLEMENTARY INFORMATION
Figure S1. Secondary structure of CAP (in the camp 2 -bound state) 10. α-helices are shown as cylinders and β- strands as arrows. Labeling of secondary structure is indicated. CDB, DBD and the hinge are
Supplemental Information. Molecular Basis of Spectral Diversity. in Near-Infrared Phytochrome-Based. Fluorescent Proteins
Chemistry & Biology, Volume 22 Supplemental Information Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins Daria M. Shcherbakova, Mikhail Baloban, Sergei Pletnev,
Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome
Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome Ahmad Jomaa 1, Yu-Hsien Hwang Fu 2, Daniel Boehringer 1, Marc Leibundgut 1, Shu-ou Shan 2, and Nenad
SUPPLEMENTARY FIGURES. Structure of the cholera toxin secretion channel in its. closed state
SUPPLEMENTARY FIGURES Structure of the cholera toxin secretion channel in its closed state Steve L. Reichow 1,3, Konstantin V. Korotkov 1,3, Wim G. J. Hol 1$ and Tamir Gonen 1,2$ 1, Department of Biochemistry
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11539 Supplementary Figure 1 Schematic representation of plant (A) and mammalian (B) P 2B -ATPase domain organization. Actuator (A-), nucleotide binding (N-),
Electron microscopy in molecular cell biology II
Electron microscopy in molecular cell biology II Cryo-EM and image processing Werner Kühlbrandt Max Planck Institute of Biophysics Sample preparation for cryo-em Preparation laboratory Specimen preparation
Supporting Information
Supporting Information Oxaliplatin binding to human copper chaperone Atox1 and protein dimerization Benny D. Belviso, 1 Angela Galliani, 2 Alessia Lasorsa, 2 Valentina Mirabelli, 1,3 Rocco Caliandro, 1
Acta Crystallographica Section D
Supporting information Acta Crystallographica Section D Volume 70 (2014) Supporting information for article: Structural characterization of the virulence factor Nuclease A from Streptococcus agalactiae
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11085 Supplementary Tables: Supplementary Table 1. Summary of crystallographic and structure refinement data Structure BRIL-NOP receptor Data collection Number of crystals 23 Space group
Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6
Supplementary Information for: Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6 Yawei Dai 1, 2, Markus Seeger 3, Jingwei Weng 4, Song Song 1, 2, Wenning Wang 4, Yan-Wen 1, 2,
SUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
Supplemental Data. Gao et al. (2012). Plant Cell /tpc
Supplemental Figure 1. Plant EMP Proteins. (A) The Accession numbers of the 12 EMP members from Arabidopsis. (B) Phylogenetic analysis of EMP proteins from Arabidopsis, human and yeast using the Mac Vector
Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism
SUPPLEMENTARY INFORMATION for: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism Daniel P. Dowling 1,2, Nathan A. Bruender 3, Anthony P. Young 3, Reid M. McCarty 3,
Table 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2
Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell
Supplemental Information. Structural and Mechanistic Paradigm. of Leptin Receptor Activation Revealed
Structure, Volume 22 Supplemental Information Structural and Mechanistic Paradigm of Leptin Receptor Activation Revealed by Complexes with Wild-Type and Antagonist Leptins Kedar Moharana, Lennart Zabeau,
SUPPLEMENTARY INFORMATION
Dph2 SeMet (iron-free) # Dph2 (iron-free) Dph2-[4Fe-4S] Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 58.26, 82.08, 160.42 58.74, 81.87, 160.01 55.70, 80.53,
Supplementary information
Supplementary information The structural basis of modularity in ECF-type ABC transporters Guus B. Erkens 1,2, Ronnie P-A. Berntsson 1,2, Faizah Fulyani 1,2, Maria Majsnerowska 1,2, Andreja Vujičić-Žagar
Automated identification of functional dynamic contact networks from X-ray crystallography
1 Automated identification of functional dynamic contact networks from X-ray crystallography Henry van den Bedem, Gira Bhabha, Kun Yang, Peter E. Wright and James S. Fraser Supplementary Figure 1 Supplementary
ParM filament images were extracted and from the electron micrographs and
Supplemental methods Outline of the EM reconstruction: ParM filament images were extracted and from the electron micrographs and straightened. The digitized images were corrected for the phase of the Contrast
Supplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two
Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for
SUPPLEMENTARY INFORMATION
Data collection Supplementary Table 1 Statistics of data collection, phasing and refinement Native Se-MAD Space group P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 50.4, 94.2, 115.4 49.8, 94.2,
ml. ph 7.5 ph 6.5 ph 5.5 ph 4.5. β 2 AR-Gs complex + GDP β 2 AR-Gs complex + GTPγS
a UV28 absorption (mau) 9 8 7 5 3 β 2 AR-Gs complex β 2 AR-Gs complex + GDP β 2 AR-Gs complex + GTPγS β 2 AR-Gs complex dissociated complex excess nucleotides b 9 8 7 5 3 β 2 AR-Gs complex β 2 AR-Gs complex
Measuring quaternary structure similarity using global versus local measures.
Supplementary Figure 1 Measuring quaternary structure similarity using global versus local measures. (a) Structural similarity of two protein complexes can be inferred from a global superposition, which
Supporting Information
Supporting Information Control of methylglyoxal synthesis in Bacillus subtilis: Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh Achim
SUPPLEMENTARY INFORMATION
doi:1.138/nature1737 Supplementary Table 1 variant Description FSEC - 2B12 a FSEC - 6A1 a K d (leucine) c Leucine uptake e K (wild-type like) K (Y18F) K (TS) K (TSY) K288A mutant, lipid facing side chain
Structural basis of PROTAC cooperative recognition for selective protein degradation
SUPPLEMENTARY INFORMATION Structural basis of PROTAC cooperative recognition for selective protein degradation Morgan S. Gadd 1, Andrea Testa 1, Xavier Lucas 1, Kwok-Ho Chan, Wenzhang Chen, Douglas J.
Chapter 6. The interaction of Src SH2 with the focal adhesion kinase catalytic domain studied by NMR
The interaction of Src SH2 with the focal adhesion kinase catalytic domain studied by NMR 103 Abstract The interaction of the Src SH2 domain with the catalytic domain of FAK, including the Y397 SH2 domain
Structural insights into Aspergillus fumigatus lectin specificity - AFL binding sites are functionally non-equivalent
Acta Cryst. (2015). D71, doi:10.1107/s1399004714026595 Supporting information Volume 71 (2015) Supporting information for article: Structural insights into Aspergillus fumigatus lectin specificity - AFL
Molecular symmetry and arrangement of subunits in extracellular hemoglobin from the nematode Ascaris mum
Eur. J. Biochem. 201, 169-173 (1991) @, FEBS 1991 001429569100618V Molecular symmetry and arrangement of subunits in extracellular hemoglobin from the nematode Ascaris mum Saleh DARAWSHE and Ezra DANlEL
Heptad-Specific Phosphorylation of RNA Polymerase II CTD
olecular Cell Supplemental Information Heptad-Specific Phosphorylation of RNA Polymerase II CTD Roland Schüller, Ignasi Forné, Tobias Straub, Amelie Schreieck, Yves Texier, Nilay Shah, Tim-ichael Decker,
Watanabe'et'al.' Supplementary'Figure'1'
MW IN O 80 2 IN O 80 SW 3 R -C 3 MW SW R -C SW 1 R -C 2 IN O 80 1 Supplementary'Figure'1' Supplementary Figure 1. SDS-PAGE image of INO80-C and SWR-C. Three independent preparations of each TAP-tagged
Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS
Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS CNS input file generatemetal.inp: remarks file generate/generatemetal.inp