+Open data
-Basic information
Entry | Database: PDB / ID: 3rpg | ||||||
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Title | Bmi1/Ring1b-UbcH5c complex structure | ||||||
Components |
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Keywords | LIGASE / Ubiquitin Ligase | ||||||
Function / homology | Function and homology information histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / SUMOylation of DNA methylation proteins / protein K11-linked ubiquitination / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression, epigenetic / : / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / ubiquitin conjugating enzyme activity / Transcriptional Regulation by E2F6 / protein monoubiquitination / germ cell development / MLL1 complex / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / heterochromatin / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / positive regulation of B cell proliferation / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / apoptotic signaling pathway / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / brain development / protein modification process / euchromatin / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of DNA-binding transcription factor activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of fibroblast proliferation / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / gene expression / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / protein ubiquitination / nuclear body / endosome membrane / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / apoptotic process / chromatin binding / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6485 Å | ||||||
Authors | Bentley, M.L. / Dong, K.C. / Cochran, A.G. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex. Authors: Bentley, M.L. / Corn, J.E. / Dong, K.C. / Phung, Q. / Cheung, T.K. / Cochran, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rpg.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rpg.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3rpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/3rpg ftp://data.pdbj.org/pub/pdb/validation_reports/rp/3rpg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 16832.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli (E. coli) / References: UniProt: P61077, ubiquitin-protein ligase | ||
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#2: Protein | Mass: 13653.970 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P35226 | ||
#3: Protein | Mass: 13514.729 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Escherichia coli (E. coli) References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 23, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.6485→50 Å / Num. all: 15512 / Num. obs: 15512 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.6485→2.74 Å / Rmerge(I) obs: 0.459 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H0D AND 2FUH Resolution: 2.6485→35.822 Å / SU ML: 0.31 / σ(F): 1.89 / Phase error: 25.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.995 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6485→35.822 Å
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Refine LS restraints |
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LS refinement shell |
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