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Open data
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Basic information
Entry | Database: PDB / ID: 3rpg | ||||||
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Title | Bmi1/Ring1b-UbcH5c complex structure | ||||||
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![]() | LIGASE / Ubiquitin Ligase | ||||||
Function / homology | ![]() histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of immature T cell proliferation in thymus / Signaling by BMP / protein K6-linked ubiquitination / 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 / Transcriptional Regulation by E2F6 / germ cell development / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / MLL1 complex / negative regulation of BMP signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / heterochromatin / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / ubiquitin ligase complex / 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 / Peroxisomal protein import / apoptotic signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / euchromatin / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of DNA-binding transcription factor activity / brain development / 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 / Neddylation / mitotic cell cycle / gene expression / ubiquitin-dependent protein catabolic process / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / endosome membrane / protein ubiquitination / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / apoptotic process / ubiquitin protein ligase binding / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bentley, M.L. / Dong, K.C. / Cochran, A.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.7 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||
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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.) ![]() ![]() ![]() | ||
#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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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