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Yorodumi- PDB-4o62: CW-type zinc finger of ZCWPW2 in complex with the amino terminus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o62 | ||||||
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Title | CW-type zinc finger of ZCWPW2 in complex with the amino terminus of histone H3 | ||||||
Components |
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Keywords | METAL/DNA BINDING PROTEIN / zinc finger / histone / Structural Genomics / Structural Genomics Consortium / SGC / METAL-DNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes ...nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Liu, Y. / Tempel, W. / Dong, A. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins. Authors: Liu, Y. / Tempel, W. / Zhang, Q. / Liang, X. / Loppnau, P. / Qin, S. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o62.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o62.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 4o62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/4o62 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/4o62 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
#1: Protein | Mass: 7078.734 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 21-78 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZCWPW2 / Plasmid: pET28a-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-V2R-pRARE2 / References: UniProt: Q504Y3 #2: Protein/peptide | | Mass: 1293.516 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-12 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: K7ES00, UniProt: P84243*PLUS #3: Chemical | #4: Chemical | ChemComp-UNX / #5: 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: 4.6 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 2 M ammonium sulfate, 2% PEG400, 0.1 M sodium HEPES, pH 7.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28303 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28303 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→41.46 Å / Num. obs: 36371 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 1.5 / Num. measured all: 11373 / Num. unique all: 2051 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→41.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1777 / WRfactor Rwork: 0.1557 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8528 / SU B: 3.963 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0728 / SU Rfree: 0.0739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: MODEL AUTO BUILDING WAS PERFORMED WIT ARP/WARP. MANUAL MODEL BUILDING WAS DONE IN COOT. MODEL GEOMETRY WAS VALIDATED WITH MOLPROBITY.
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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 max: 99.64 Å2 / Biso mean: 36.6352 Å2 / Biso min: 17.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→41.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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