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Open data
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Basic information
Entry | Database: PDB / ID: 3mev | ||||||
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Title | Crystal structure of SGF29 in complex with R2AK4me3 | ||||||
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![]() | TRANSCRIPTION / Structural Genomics Consortium / SGC / Nucleus / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.5 KB | Display | ![]() |
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Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lx7C ![]() 3me9C ![]() 3meaC ![]() 3metC ![]() 3meuC ![]() 3mewC ![]() 3mp1C ![]() 3mp6C ![]() 3mp8C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 890.039 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-9 / Source method: obtained synthetically / Details: R2AK4me3 8MER / Source: (synth.) ![]() #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.15 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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: 1.83→55.25 Å / Num. obs: 29380 / % possible obs: 95.2 % / Redundancy: 7.2 % / Rsym value: 0.057 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 5.96 / Rsym value: 0.224 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 28.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→31.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Total num. of bins used: 20
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