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⇱ RCSB PDB - 2H0D: Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex


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Computed Structure Models (CSM)

 2H0D | pdb_00002h0d

Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a Bmi-1-Ring1B Polycomb Group Ubiquitin Ligase Complex.

Li, Z.Cao, R.Wang, M.Myers, M.P.Zhang, Y.Xu, R.M.

(2006) J Biological Chem 281: 20643-20649

  • PubMed16714294 Search on PubMed
  • DOI: https://doi.org/10.1074/jbc.M602461200
  • Primary Citation Related Structures: 
    2H0D

  • PubMed Abstract: 

    Polycomb group proteins Bmi-1 and Ring1B are core subunits of the PRC1 complex, which plays important roles in the regulation of Hox gene expression, X-chromosome inactivation, tumorigenesis, and stem cell self-renewal. The RING finger protein Ring1B is an E3 ligase that participates in the ubiquitination of lysine 119 of histone H2A, and the binding of Bmi-1 stimulates the E3 ligase activity. We have mapped the regions of Bmi-1 and Ring1B required for efficient ubiquitin transfer and determined a 2.5-A structure of the Bmi-1-Ring1B core domain complex. The structure reveals that Ring1B "hugs" Bmi-1 through extensive RING domain contacts and its N-terminal tail wraps around Bmi-1. The two regions of interaction have a synergistic effect on the E3 ligase activity. Our analyses suggest a model where the Bmi-1-Ring1B complex stabilizes the interaction between the E2 enzyme and the nucleosomal substrate to allow efficient ubiquitin transfer.


  • Organizational Affiliation
    • Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

Macromolecule Content 

  • Total Structure Weight: 23.11 kDa 
  • Atom Count: 1,624 
  • Modeled Residue Count: 197 
  • Deposited Residue Count: 197 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B lymphoma Mo-MLV insertion region97Homo sapiensMutation(s): 0 
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UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens)
Explore P35226 
Go to UniProtKB:  P35226
PHAROS:  P35226
GTEx:  ENSG00000168283 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35226
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin ligase protein RING2100Homo sapiensMutation(s): 0 
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens)
Explore Q99496 
Go to UniProtKB:  Q99496
PHAROS:  Q99496
GTEx:  ENSG00000121481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99496
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.514α = 90
b = 120.514β = 90
c = 27.209γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MADNESSdata reduction

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

  • Released Date: 2006-05-23 
  • Deposition Author(s): Xu, R.M.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.