[English] 日本語
Yorodumi- PDB-3ql9: Monoclinic complex structure of ATRX ADD bound to histone H3K9me3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ql9 | ||||||
---|---|---|---|---|---|---|---|
Title | Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/STRUCTURAL PROTEIN / zinc finger / transcription / histone / lysine trimethylation / nuclear protein / HISTONE-BINDING PROTEIN / TRANSCRIPTION-STRUCTURAL PROTEIN complex | ||||||
Function / homology | Function and homology information post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body ...post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / meiotic spindle organization / cellular response to hydroxyurea / DNA translocase activity / muscle cell differentiation / chromo shadow domain binding / pericentric heterochromatin formation / positive regulation of telomere maintenance / inner kinetochore / condensed chromosome, centromeric region / ATP-dependent chromatin remodeler activity / oocyte maturation / protein localization to chromosome, telomeric region / nuclear chromosome / nucleus organization / seminiferous tubule development / replication fork processing / spermatid development / DNA damage response, signal transduction by p53 class mediator / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / forebrain development / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / helicase activity / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / chromatin DNA binding / PML body / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / cell population proliferation / transcription by RNA polymerase II / chromosome, telomeric region / nuclear body / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å | ||||||
Authors | Xiang, B. / Li, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome Authors: Iwase, S. / Xiang, B. / Ghosh, S. / Ren, T. / Lewis, P.W. / Cochrane, J.C. / Allis, C.D. / Picketts, D.J. / Patel, D.J. / Li, H. / Shi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ql9.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ql9.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ql9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ql9_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ql9_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 3ql9_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3ql9_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/3ql9 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/3ql9 | HTTPS FTP |
-Related structure data
Related structure data | 3qlaC 3qlcC 3qlnSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14793.869 Da / Num. of mol.: 1 / Fragment: N-terminal ADD domain, UNP residues 167-289 / Mutation: K251R, F284Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P46100, DNA helicase | ||
---|---|---|---|
#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 Fragment: K9 trimethylated H3 N-terminal fragment, UNP residues 2-16 Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.15 % / Mosaicity: 0.129 ° |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.93→50 Å / Num. obs: 77964 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.08 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QLN Resolution: 0.93→21.95 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.9504 / SU ML: 0.1 / σ(F): 0 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.962 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.95 Å2 / Biso mean: 9.9856 Å2 / Biso min: 2.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.93→21.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
|