+Open data
-Basic information
Entry | Database: PDB / ID: 7m10 | ||||||
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Title | PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 | ||||||
Components |
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Keywords | PROTEIN BINDING / PHD FINGER / METAL-BINDING / ZINC-FINGER / HISTONE-BINDING / NON-HISTONE BINDING | ||||||
Function / homology | Function and homology information histone H4K20 demethylase activity / Golgi disassembly / histone H3T3 kinase activity / negative regulation of rDNA heterochromatin formation / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / protein demethylation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / Golgi stack ...histone H4K20 demethylase activity / Golgi disassembly / histone H3T3 kinase activity / negative regulation of rDNA heterochromatin formation / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / protein demethylation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones / kinetochore / kinase activity / histone binding / protein autophosphorylation / transcription coactivator activity / non-specific serine/threonine protein kinase / protein kinase activity / iron ion binding / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem.J. / Year: 2021 Title: Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions. Authors: Chen, J. / Horton, J. / Sagum, C. / Zhou, J. / Cheng, X. / Bedford, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m10.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m10.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 7m10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/7m10 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/7m10 | HTTPS FTP |
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-Related structure data
Related structure data | 3kqiS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8535.833 Da / Num. of mol.: 1 / Fragment: PHD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF2, CENP-35, KIAA0662 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold plus References: UniProt: O75151, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor | ||||||
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#2: Protein/peptide | Mass: 1313.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q99986, non-specific serine/threonine protein kinase | ||||||
#3: Chemical | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 3.5M Sodium Formate,100mM TRIS pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→32.5 Å / Num. obs: 33230 / % possible obs: 81.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 9.83 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 991 / CC1/2: 0.74 / CC star: 0.922 / Rpim(I) all: 0.37 / % possible all: 24.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KQI Resolution: 1.15→32.5 Å / SU ML: 0.107 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8546 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→32.5 Å
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Refine LS restraints |
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LS refinement shell |
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