+Open data
-Basic information
Entry | Database: PDB / ID: 4nft | ||||||
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Title | Crystal structure of human lnkH2B-h2A.Z-Anp32e | ||||||
Components |
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Keywords | CHAPERONE / Histone binding protein | ||||||
Function / homology | Function and homology information phosphatase inhibitor activity / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / protein folding chaperone / Recognition and association of DNA glycosylase with site containing an affected purine ...phosphatase inhibitor activity / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates 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 / 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 / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / histone binding / Senescence-Associated Secretory Phenotype (SASP) / cytoplasmic vesicle / regulation of apoptotic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / 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: 2.61 Å | ||||||
Authors | Shan, S. / Pan, L. / Mao, Z. / Wang, W. / Sun, J. / Dong, Q. / Liang, X. / Ding, X. / Chen, S. / Dai, L. ...Shan, S. / Pan, L. / Mao, Z. / Wang, W. / Sun, J. / Dong, Q. / Liang, X. / Ding, X. / Chen, S. / Dai, L. / Zhang, Z. / Zhu, B. / Zhou, Z. | ||||||
Citation | Journal: Cell Res. / Year: 2014 Title: Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z Authors: Mao, Z. / Pan, L. / Wang, W. / Sun, J. / Shan, S. / Dong, Q. / Liang, X. / Dai, L. / Ding, X. / Chen, S. / Zhang, Z. / Zhu, B. / Zhou, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nft.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nft.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nft ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nft | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22508.875 Da / Num. of mol.: 4 / Fragment: UNP residues 34-126, 16-114 Source method: isolated from a genetically manipulated source Details: Chimera of H2B and H2A.Z / Source: (gene. exp.) Homo sapiens (human) / Gene: H2BFQ, H2AZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q16778, UniProt: P0C0S5 #2: Protein | Mass: 6027.800 Da / Num. of mol.: 2 / Fragment: UNP residues 185-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANP32E / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BTT0 #3: 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: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 29217 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 31.81 Å2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→39.795 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.5309 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 46.87 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.73 Å2 / Biso mean: 31.3547 Å2 / Biso min: 12.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→39.795 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: 11
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