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- PDB-3rpg: Bmi1/Ring1b-UbcH5c complex structure -

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Basic information

Entry
Database: PDB / ID: 3rpg
TitleBmi1/Ring1b-UbcH5c complex structure
Components
  • E3 ubiquitin-protein ligase RING2
  • Polycomb complex protein BMI-1
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsLIGASE / Ubiquitin Ligase
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / regulation of adaxial/abaxial pattern formation ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / regulation of adaxial/abaxial pattern formation / sex chromatin / PcG protein complex / positive regulation of immature T cell proliferation in thymus / Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / protein K11-linked ubiquitination / SUMOylation of RNA binding proteins / anterior/posterior axis specification / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / germ cell development / ubiquitin conjugating enzyme activity / humoral immune response / hemopoiesis / MLL1 complex / negative regulation of apoptotic signaling pathway / cellular response to interleukin-1 / negative regulation of BMP signaling pathway / protein monoubiquitination / ubiquitin ligase complex / cellular response to dexamethasone stimulus / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / protein K48-linked ubiquitination / heterochromatin / protein autoubiquitination / positive regulation of B cell proliferation / SUMOylation of transcription cofactors / TICAM1, RIP1-mediated IKK complex recruitment / SUMOylation of chromatin organization proteins / epigenetic regulation of gene expression / IKK complex recruitment mediated by RIP1 / Regulation of PTEN gene transcription / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / apoptotic signaling pathway / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / euchromatin / Inactivation of CSF3 (G-CSF) signaling / brain development / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / positive regulation of fibroblast proliferation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / regulation of gene expression / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / gene expression / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / nuclear body / chromatin remodeling / DNA repair / apoptotic process / chromatin binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polycomb complex protein BMI-1 / Ubiquitin-conjugating enzyme E2 D3 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6485 Å
AuthorsBentley, M.L. / Dong, K.C. / Cochran, A.G.
CitationJournal: 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
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D3
B: Polycomb complex protein BMI-1
C: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2637
Polymers44,0013
Non-polymers2624
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)16,8321
Polymers16,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Polycomb complex protein BMI-1
C: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4306
Polymers27,1692
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-28 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.890, 107.890, 77.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating ...Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


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
#2: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


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 E3 ubiquitin-protein ligase RING2 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1


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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 23, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.6485→2.74 Å / Rmerge(I) obs: 0.459 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H0D AND 2FUH

2h0d

2fuh


Resolution: 2.6485→35.822 Å / SU ML: 0.31 / σ(F): 1.89 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 771 5 %RANDOM
Rwork0.2173 ---
obs0.2186 15430 99.57 %-
Solvent computationShrinkage 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
Baniso -1Baniso -2Baniso -3
1-0.2896 Å2-0 Å20 Å2
2--0.2896 Å2-0 Å2
3----0.5792 Å2
Refinement stepCycle: LAST / Resolution: 2.6485→35.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 4 115 2912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042858
X-RAY DIFFRACTIONf_angle_d0.93876
X-RAY DIFFRACTIONf_dihedral_angle_d12.1381093
X-RAY DIFFRACTIONf_chiral_restr0.057440
X-RAY DIFFRACTIONf_plane_restr0.004492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6485-2.81440.33661330.30922401X-RAY DIFFRACTION100
2.8144-3.03160.34091260.28432411X-RAY DIFFRACTION100
3.0316-3.33650.26841200.25012404X-RAY DIFFRACTION99
3.3365-3.81880.25371380.21682443X-RAY DIFFRACTION100
3.8188-4.80950.1881260.17652437X-RAY DIFFRACTION99
4.8095-35.82550.21221280.18892563X-RAY DIFFRACTION100

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