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Yorodumi- PDB-3qlc: Complex structure of ATRX ADD domain bound to unmodified H3 1-15 ... -
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-Basic information
Entry | Database: PDB / ID: 3qlc | ||||||
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Title | Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide | ||||||
Components |
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Keywords | TRANSCRIPTION/STRUCTURAL PROTEIN / Zinc Finger / ATP-dependent chromatin remodeller / chromatin binding / lysine methylation / 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 / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Li, H. / Patel, D.J. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qlc.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qlc.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qlc_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 3qlc_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 3qlc_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3qlc_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/3qlc ftp://data.pdbj.org/pub/pdb/validation_reports/ql/3qlc | HTTPS FTP |
-Related structure data
Related structure data | 3ql9C 3qlaC 3qlnSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14793.869 Da / Num. of mol.: 2 / 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: 1565.797 Da / Num. of mol.: 2 / Fragment: N-terminal tail, 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 | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.49 % / Mosaicity: 0.25 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2010 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 18318 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Rmerge(I) obs: 0.063 / Χ2: 1.219 / Net I/σ(I): 14.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QLN Resolution: 2.5→38.054 Å / Occupancy max: 1 / Occupancy min: 0.73 / FOM work R set: 0.812 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.487 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.99 Å2 / Biso mean: 51.2267 Å2 / Biso min: 28.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.054 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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