+Open data
-Basic information
Entry | Database: PDB / ID: 3kv4 | ||||||
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Title | Structure of PHF8 in complex with histone H3 | ||||||
Components |
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Keywords | H3K4me3 binding protein / Transferase / Epigenetics / Histone code / covalent histone modifications / Jumonji demethylase / Mental retardation / Metal-binding / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I ...histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I / histone H3K9 demethylase activity / histone demethylase activity / transcription coregulator activity / nucleosomal DNA binding / methylated histone binding / Condensation of Prophase Chromosomes / HDMs demethylate histones / euchromatin / brain development / G1/S transition of mitotic cell cycle / structural constituent of chromatin / nucleosome / positive regulation of cell growth / nuclear membrane / iron ion binding / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Horton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Authors: Horton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kv4.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kv4.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kv4_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 3kv4_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 3kv4_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3kv4_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kv4 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kv4 | HTTPS FTP |
-Related structure data
Related structure data | 3kv5SC 3kv6C 3kv9C 3kvaC 3kvbC S: Starting model for refinement C: citing same article (ref.) |
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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 / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 51603.000 Da / Num. of mol.: 1 / Fragment: UNP Residues 37-483 Source method: isolated from a genetically manipulated source Details: GST-fusion / Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1111, PHF8, ZNF422 / Plasmid: pXC721 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q9UPP1, Transferases |
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#2: Protein/peptide | Mass: 2632.138 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-25 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q6NXT2 |
-Non-polymers , 6 types, 223 molecules
#3: Chemical | #4: Chemical | ChemComp-FE2 / | #5: Chemical | ChemComp-NI / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-OGA / | #8: 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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | pH: 5.6 Details: 25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→34.72 Å / Num. obs: 30847 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KV5 Resolution: 2.19→34.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 239337.86 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.6317 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→34.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.27 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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