+Open data
-Basic information
Entry | Database: PDB / ID: 4hpm | ||||||
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Title | PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex | ||||||
Components |
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Keywords | TRANSCRIPTION / POLYCOMB / BCORL1 / PCGF1 / RAWUL / NSPC1 / E3-LIGASE / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / TRANSCRIPTION REPRESSOR / LIGASE / METAL-BINDING / NUCLEUS / REPRESSOR / UBL CONJUGATION PATHWAY / ZINC-FINGER | ||||||
Function / homology | Function and homology information PRC1 complex / PcG protein complex / promoter-specific chromatin binding / transcription corepressor activity / chromatin organization / chromatin remodeling / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus ...PRC1 complex / PcG protein complex / promoter-specific chromatin binding / transcription corepressor activity / chromatin organization / chromatin remodeling / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Junco, S.E. / Wang, R. / Gaipa, J. / Taylor, A.B. / Gearhart, M.D. / Bardwell, V.J. / Hart, P.J. / Kim, C.A. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure of the Polycomb Group Protein PCGF1 in Complex with BCOR Reveals Basis for Binding Selectivity of PCGF Homologs. Authors: Junco, S.E. / Wang, R. / Gaipa, J.C. / Taylor, A.B. / Schirf, V. / Gearhart, M.D. / Bardwell, V.J. / Demeler, B. / Hart, P.J. / Kim, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hpm.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hpm.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hpm_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 4hpm_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | 4hpm_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4hpm_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/4hpm ftp://data.pdbj.org/pub/pdb/validation_reports/hp/4hpm | HTTPS FTP |
-Related structure data
Related structure data | 4hplSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14023.914 Da / Num. of mol.: 2 / Fragment: UNP residues 1594-1711 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCORL1 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5H9F3 #2: Protein | Mass: 11074.042 Da / Num. of mol.: 2 / Fragment: UNP residues 167-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSPC1, PCGF1, RNF68 / Plasmid: pet-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BSM1 #3: Chemical | ChemComp-PO4 / #4: 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: 1.95 Å3/Da / Density % sol: 36.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.71 Å / Num. obs: 32631 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4455 / Rsym value: 0.415 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HPL Resolution: 1.85→19.71 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.71 Å
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Refine LS restraints |
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LS refinement shell |
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