+Open data
-Basic information
Entry | Database: PDB / ID: 3met | ||||||
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Title | Crystal structure of SGF29 in complex with H3K4me2 | ||||||
Components |
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Keywords | TRANSCRIPTION / Structural Genomics Consortium / SGC / Nucleus / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core | ||||||
Function / homology | Function and homology information SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair ...SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / transcription initiation-coupled chromatin remodeling / methylated histone binding / response to endoplasmic reticulum stress / mitotic spindle / structural constituent of chromatin / nucleosome / HATs acetylate histones / regulation of cell cycle / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bian, C.B. / Xu, C. / Lam, R. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3met.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3met.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 3met.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/3met ftp://data.pdbj.org/pub/pdb/validation_reports/me/3met | HTTPS FTP |
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-Related structure data
Related structure data | 3lx7C 3me9C 3meaC 3meuC 3mevC 3mewC 3mp1C 3mp6C 3mp8C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 20295.742 Da / Num. of mol.: 2 / Fragment: UNP Residues 115-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC101, SGF29 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q96ES7 #2: Protein/peptide | Mass: 1278.482 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-12 / Source method: obtained synthetically / Details: H3K4me2 11mer / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133 |
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-Non-polymers , 4 types, 203 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.65 Å / Num. all: 24231 / Num. obs: 24197 |
Reflection shell | Resolution: 2→2.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.139 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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