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: 3.28 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.3 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: https://doi.org/10.1038/nature13890
  • Primary Citation of Related Structures:  
    4R8P

  • 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 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: histone H3.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: histone H4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
Gene Names: histone H2B 1.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb complex protein BMI-1
K, M
110Homo sapiensMutation(s): 0 
Gene Names: BMI1, PCGF4, RNF51
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
L, N
268Homo sapiensMutation(s): 0 
Gene Names: BAP1, DING, HIPI3, RING1B, Ring1B-UbcH5c fusion, RNF2, UBC5C, UBCH5C, UBE2D3
EC: 6.3.2 (PDB Primary Data), 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt), 2.3.2.27 (UniProt)
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Find proteins for P61077 (Homo sapiens)
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UniProt GroupsP61077Q99496
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-mer)147synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-mer)147synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.923α = 90
b = 180.049β = 90
c = 375.251γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description