+Open data
-Basic information
Entry | Database: PDB / ID: 4au7 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of the Suv4-20h2 ternary complex with histone H4 | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / EPIGENETICS | ||||||
Function / homology | Function and homology information : / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / DNA Damage/Telomere Stress Induced Senescence / SUMOylation of chromatin organization proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...: / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / DNA Damage/Telomere Stress Induced Senescence / SUMOylation of chromatin organization proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / G2/M DNA damage checkpoint / HDMs demethylate histones / [histone H4]-lysine20 N-methyltransferase / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / HDACs deacetylate histones / : / histone H4K20 methyltransferase activity / Processing of DNA double-strand break ends / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / positive regulation of isotype switching / Estrogen-dependent gene expression / S-adenosyl-L-methionine binding / positive regulation of double-strand break repair via nonhomologous end joining / protein localization to CENP-A containing chromatin / pericentric heterochromatin / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / protein heterodimerization activity / DNA repair / chromatin binding / DNA binding / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Southall, S.M. / Cronin, N.B. / Wilson, J.R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: A Novel Route to Product Specificity in the Suv4-20 Family of Histone H4K20 Methyltransferases. Authors: Southall, S.M. / Cronin, N.B. / Wilson, J.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4au7.cif.gz | 203 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4au7.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 4au7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4au7 ftp://data.pdbj.org/pub/pdb/validation_reports/au/4au7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bupC 3rq4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 28162.127 Da / Num. of mol.: 2 / Fragment: SET DOMAIN, RESIDUES 1-246 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q6Q783, histone-lysine N-methyltransferase #2: Protein/peptide | | Mass: 1274.519 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-26 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P62806 |
---|
-Non-polymers , 4 types, 167 molecules
#3: Chemical | ChemComp-SAH / | ||||
---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | FIRST RESIDUE FROM VECTOR |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 44.8 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0081 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2012 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0081 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.3 Å / Num. obs: 29593 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 82 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RQ4 Resolution: 2.07→55.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.589 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE C-TERMINUS OF MOECULE B IS DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.003 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→55.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|