[English] 日本語
Yorodumi- PDB-3iid: Crystal structure of the macro domain of human histone macroH2A1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iid | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form A) | ||||||
Components | Core histone macro-H2A.1, Isoform 1 | ||||||
Keywords | GENE REGULATION / Histone / Chromatin / macro domain / Chromatin regulator / Chromosomal protein / DNA-binding / Isopeptide bond / Methylation / Nucleosome core / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex chromatin ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex chromatin / sex-chromosome dosage compensation / positive regulation of endodermal cell differentiation / establishment of protein localization to chromatin / double-stranded methylated DNA binding / Barr body / rDNA binding / negative regulation of protein serine/threonine kinase activity / regulation of oxidative phosphorylation / positive regulation of keratinocyte differentiation / poly-ADP-D-ribose modification-dependent protein binding / protein serine/threonine kinase inhibitor activity / negative regulation of response to oxidative stress / nuclear chromosome / condensed chromosome / negative regulation of gene expression, epigenetic / site of DNA damage / regulation of lipid metabolic process / pericentric heterochromatin / nucleosomal DNA binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / heterochromatin formation / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / chromatin / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hothorn, M. / Bortfeld, M. / Ladurner, A.G. / Scheffzek, K. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Authors: Timinszky, G. / Till, S. / Hassa, P.O. / Hothorn, M. / Kustatscher, G. / Nijmeijer, B. / Colombelli, J. / Altmeyer, M. / Stelzer, E.H. / Scheffzek, K. / Hottiger, M.O. / Ladurner, A.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3iid.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3iid.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 3iid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iid_validation.pdf.gz | 795.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3iid_full_validation.pdf.gz | 800.3 KB | Display | |
Data in XML | 3iid_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 3iid_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/3iid ftp://data.pdbj.org/pub/pdb/validation_reports/ii/3iid | HTTPS FTP |
-Related structure data
Related structure data | 3iifC 1zr3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22274.334 Da / Num. of mol.: 1 / Fragment: Macro domain: UNP residues 162-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFY, MACROH2A1, macroH2A1.1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O75367-2, UniProt: O75367*PLUS |
---|---|
#2: Chemical | ChemComp-APR / |
#3: Chemical | ChemComp-NO3 / |
#4: 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: 50.02 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 35% PEG 1000, 0.2 M K2NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2006 |
Radiation | Monochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.86 Å / Num. all: 17128 / Num. obs: 17128 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Redundancy: 10 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.057 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1220 / Rsym value: 0.525 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZR3 Resolution: 1.9→19.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.801 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.866 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|