+Open data
-Basic information
Entry | Database: PDB / ID: 4cay | ||||||
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Title | Crystal structure of a human Anp32e-H2A.Z-H2B complex | ||||||
Components |
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Keywords | TRANSCRIPTION / EPIGENETICS / NUCLEOSOME / HISTONE VARIANT / HISTONE CHAPERONE | ||||||
Function / homology | Function and homology information phosphatase inhibitor activity / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...phosphatase inhibitor activity / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / protein folding chaperone / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to estradiol stimulus / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / 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 / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / histone binding / cytoplasmic vesicle / Senescence-Associated Secretory Phenotype (SASP) / regulation of apoptotic process / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / Ub-specific processing proteases / defense response to Gram-positive bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Obri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Mak, T.W. ...Obri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Mak, T.W. / Dimitrov, S. / Romier, C. / Hamiche, A. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Anp32E is a Histone Chaperone that Removes H2A.Z from Chromatin Authors: Obri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Wak, T.W. / Dimitrov, S. / Romier, C. / Hamiche, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cay.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cay.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/4cay ftp://data.pdbj.org/pub/pdb/validation_reports/ca/4cay | HTTPS FTP |
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-Related structure data
Related structure data | 1f66S 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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Unit cell |
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-Components
#1: Protein | Mass: 12020.978 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN, RESIDUES 19-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C0S5 |
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#2: Protein | Mass: 10881.576 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN, RESIDUES 31-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899 |
#3: Protein/peptide | Mass: 3493.605 Da / Num. of mol.: 1 / Fragment: H2A.Z INTERACTING DOMAIN (ZID), RESIDUES 215-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BTT0 |
#4: Water | ChemComp-HOH / |
Sequence details | THE METHIONINE AT THE START OF THE MACROMOLECULAR SEQUENCE (CHAIN A) IS AN EXPRESSION ARTEFACT THE ...THE METHIONINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA CACODYLATE, PH 7.0, 0.2 M NA FORMATE, 24% TO 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. obs: 30963 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 16.54 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F66 Resolution: 1.48→37.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.9516 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso mean: 23.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.189 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→37.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.53 Å / Total num. of bins used: 15
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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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