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Yorodumi- PDB-5t8r: Crystal structure of human BAZ2A PHD zinc finger in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 5t8r | ||||||
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Title | Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer | ||||||
Components |
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Keywords | TRANSCRIPTION / PHD zinc fingers / histone3 / complex | ||||||
Function / homology | Function and homology information NoRC complex / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / Chromatin modifying enzymes / heterochromatin formation / epigenetic regulation of gene expression ...NoRC complex / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / Chromatin modifying enzymes / heterochromatin formation / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / 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) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / nuclear receptor binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / 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 / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear speck / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Amato, A. / Gadd, M.S. / Bortoluzzi, A. / Ciulli, A. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains. Authors: Bortoluzzi, A. / Amato, A. / Lucas, X. / Blank, M. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t8r.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8r.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 5t8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t8r_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 5t8r_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 5t8r_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5t8r_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8r ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8r | HTTPS FTP |
-Related structure data
Related structure data | 4qf2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDEG
#1: Protein | Mass: 6597.694 Da / Num. of mol.: 4 / Fragment: PHD domain, UNP residues 1673-1728 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9 #2: Protein/peptide | Mass: 1150.332 Da / Num. of mol.: 2 / Fragment: UNP residues 2-11 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 |
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-Non-polymers , 4 types, 107 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2 M Na/K phosphate / PH range: 8 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→45.62 Å / Num. obs: 10901 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.3 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4qf2 Resolution: 2.4→45.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.647 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.245 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 500 Å2 / Biso mean: 52.134 Å2 / Biso min: 22.3 Å2
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Refinement step | Cycle: final / Resolution: 2.4→45.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 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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