5HYN

Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report



Literature

Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2.

Justin, N.Zhang, Y.Tarricone, C.Martin, S.R.Chen, S.Underwood, E.De Marco, V.Haire, L.F.Walker, P.A.Reinberg, D.Wilson, J.R.Gamblin, S.J.

(2016) Nat Commun 7: 11316-11316

  • DOI: 10.1038/ncomms11316
  • Primary Citation of Related Structures:  
    5HYN

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2) silences gene expression through trimethylation of K27 of histone H3 (H3K27me3) via its catalytic SET domain. A missense mutation in the substrate of PRC2, histone H3K27M, is associated with certain pediatric brain cancers and is linked to a global decrease of H3K27me3 in the affected cells thought to be mediated by inhibition of PRC2 activity ...

    Polycomb repressive complex 2 (PRC2) silences gene expression through trimethylation of K27 of histone H3 (H3K27me3) via its catalytic SET domain. A missense mutation in the substrate of PRC2, histone H3K27M, is associated with certain pediatric brain cancers and is linked to a global decrease of H3K27me3 in the affected cells thought to be mediated by inhibition of PRC2 activity. We present here the crystal structure of human PRC2 in complex with the inhibitory H3K27M peptide bound to the active site of the SET domain, with the methionine residue located in the pocket that normally accommodates the target lysine residue. The structure and binding studies suggest a mechanism for the oncogenic inhibition of H3K27M. The structure also reveals how binding of repressive marks, like H3K27me3, to the EED subunit of the complex leads to enhancement of the catalytic efficiency of the SET domain and thus the propagation of this repressive histone modification.


    Organizational Affiliation

    The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2AFKQ746Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.356 (UniProt)
Find proteins for Q15910 (Homo sapiens)
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PHAROS  Q15910
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein EEDBGLR367Homo sapiensMutation(s): 0 
Gene Names: EED
Find proteins for O75530 (Homo sapiens)
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PHAROS  O75530
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
JARID2 K116me3EJPU12Homo sapiensMutation(s): 0 
Gene Names: JARID2JMJ
Find proteins for Q92833 (Homo sapiens)
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PHAROS  Q92833
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein SUZ12CHMS129Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
Find proteins for Q15022 (Homo sapiens)
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PHAROS  Q15022
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
H3K27MDIOT13Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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PHAROS  P68431
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, F, K, Q
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, F, K, Q
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E,J,P,UL-PEPTIDE LINKINGC9 H21 N2 O2LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHIC50:  4800   nM  BindingDB
SAHIC50:  263   nM  BindingDB
SAHIC50:  283   nM  BindingDB
SAHIC50:  6908.2001953125   nM  BindingDB
SAHIC50:  16619.30078125   nM  BindingDB
SAHIC50:  263   nM  BindingDB
SAHIC50:  6237.89990234375   nM  BindingDB
SAHIC50:  11000   nM  BindingDB
SAHIC50:  5903.39990234375   nM  BindingDB
SAHIC50:  380   nM  BindingDB
SAHIC50:  467   nM  BindingDB
SAHIC50:  380   nM  BindingDB
SAHIC50:  4800   nM  BindingDB
SAHIC50:  283   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.64α = 90
b = 171.51β = 90
c = 274.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Francis Crick InstituteUnited Kingdom10078

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release