+Open data
-Basic information
Entry | Database: PDB / ID: 4zbj | |||||||||
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Title | UBN1 peptide bound to H3.3/H4/Asf1 | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Histone Chaperone / Complex / Chromatin Assembly | |||||||||
Function / homology | Function and homology information : / : / : / Formation of the beta-catenin:TCF transactivating complex / Factors involved in megakaryocyte development and platelet production / chromatin organization => GO:0006325 / Oxidative Stress Induced Senescence / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...: / : / : / Formation of the beta-catenin:TCF transactivating complex / Factors involved in megakaryocyte development and platelet production / chromatin organization => GO:0006325 / Oxidative Stress Induced Senescence / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Condensation of Prophase Chromosomes / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / negative regulation of DNA damage checkpoint / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / subtelomeric heterochromatin formation / bicellular tight junction / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / viral process / regulation of protein phosphorylation / protein modification process / PML body / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / nuclear body / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Xenopus laevis (African clawed frog) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | |||||||||
Authors | Marmorstein, R. / Ricketts, M.D. / Tang, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2015 Title: Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex. Authors: Daniel Ricketts, M. / Frederick, B. / Hoff, H. / Tang, Y. / Schultz, D.C. / Singh Rai, T. / Grazia Vizioli, M. / Adams, P.D. / Marmorstein, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zbj.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zbj.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zbj_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 4zbj_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 4zbj_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4zbj_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbj ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbj | HTTPS FTP |
-Related structure data
Related structure data | 2hueS 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 19663.973 Da / Num. of mol.: 1 / Fragment: UNP residues 2-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P32447 |
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#2: Protein | Mass: 8812.344 Da / Num. of mol.: 1 / Fragment: UNP residues 62-136 / Mutation: G103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q10453, UniProt: Q6PI79*PLUS |
#3: Protein | Mass: 9540.251 Da / Num. of mol.: 1 / Fragment: UNP residues 21-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 3144.248 Da / Num. of mol.: 1 / Fragment: UNP residues 122-148 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NPG3 |
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-Non-polymers , 3 types, 167 molecules
#5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MPD / ( | #7: 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: 3.43 Å3/Da / Density % sol: 64.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Sodium Cacodylate pH 6.0, 8% PEG 8K, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→25.406 Å / Num. obs: 26431 / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HUE Resolution: 2.248→25.406 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 26.86 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.248→25.406 Å
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Refine LS restraints |
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LS refinement shell |
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