4R8P

Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2846 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.

McGinty, R.K.Henrici, R.C.Tan, S.

(2014) Nature 514: 591-596

  • DOI: 10.1038/nature13890

  • PubMed Abstract: 
  • The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiqui ...

    The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the human Ring1B-Bmi1-UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with several nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.


    Organizational Affiliation

    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisN/A
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisN/A
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevisN/A
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisN/A
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Polycomb complex protein BMI-1
K, M
110Homo sapiensGene Names: BMI1 (PCGF4, RNF51)
Find proteins for P35226 (Homo sapiens)
Go to Gene View: BMI1
Go to UniProtKB:  P35226
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
L, N
268Homo sapiensGene Names: UBE2D3 (UBC5C, UBCH5C), RNF2 (BAP1, DING, HIPI3, RING1B)
EC: 2.3.2.23, 2.3.2.24 6.3.2.-
Find proteins for P61077 (Homo sapiens)
Go to Gene View: UBE2D3
Go to UniProtKB:  P61077
Find proteins for Q99496 (Homo sapiens)
Go to Gene View: RNF2
Go to UniProtKB:  Q99496
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-mer)I147synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-mer)J147synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K, L, M, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2846 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.923α = 90.00
b = 180.049β = 90.00
c = 375.251γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy