+Open data
-Basic information
Entry | Database: PDB / ID: 5y8v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GAS41 | ||||||
Components | YEATS domain-containing protein 4 | ||||||
Keywords | NUCLEAR PROTEIN / YEATS domain | ||||||
Function / homology | Function and homology information modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / histone binding / nuclear membrane / regulation of apoptotic process / chromatin remodeling / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Wang, Y. / Hao, Q. | ||||||
Funding support | Hong Kong, 1items
| ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation Authors: Wang, Y. / Jin, J. / Chung, M.W.H. / Feng, L. / Sun, H. / Hao, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5y8v.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5y8v.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y8v_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5y8v_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5y8v_validation.xml.gz | 23 KB | Display | |
Data in CIF | 5y8v_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/5y8v ftp://data.pdbj.org/pub/pdb/validation_reports/y8/5y8v | HTTPS FTP |
-Related structure data
Related structure data | 3fk3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16565.041 Da / Num. of mol.: 4 / Fragment: UNP residues 21-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: O95619 #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % |
---|---|
Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6 / Details: 0.1M MES pH 6.5, 1.6M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 19176 / % possible obs: 98.7 % / Redundancy: 3.5 % / Net I/σ(I): 9.51 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FK3 Resolution: 2.61→31.495 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.9
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→31.495 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|