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 

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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 EZH2A, F, K, P [auth Q]746Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.356 (UniProt)
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Find proteins for Q15910 (Homo sapiens)
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PHAROS:  Q15910
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein EEDB, G, L, Q [auth R]367Homo sapiensMutation(s): 0 
Gene Names: EED
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Find proteins for O75530 (Homo sapiens)
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PHAROS:  O75530
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein SUZ12C, H, M, R [auth S]129Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
H3K27MD, I, N [auth O], S [auth T]13Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
JARID2 K116me3E, J, O [auth P], T [auth U]12Homo sapiensMutation(s): 0 
Gene Names: JARID2JMJ
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
CA [auth A], DB [auth Q], LA [auth F], UA [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth Q] , BA [auth A] , BB [auth Q] , CB [auth Q] , DA [auth F] , EA [auth F] , FA [auth F] , 
AA [auth A],  AB [auth Q],  BA [auth A],  BB [auth Q],  CB [auth Q],  DA [auth F],  EA [auth F],  FA [auth F],  GA [auth F],  HA [auth F],  IA [auth F],  JA [auth F],  KA [auth F],  MA [auth K],  NA [auth K],  OA [auth K],  PA [auth K],  QA [auth K],  RA [auth K],  SA [auth K],  TA [auth K],  U [auth A],  V [auth A],  VA [auth Q],  W [auth A],  WA [auth Q],  X [auth A],  XA [auth Q],  Y [auth A],  YA [auth Q],  Z [auth A],  ZA [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E, J, O [auth P], T [auth U]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  5HYN IC50: min: 263, max: 6.50e+4 (nM) from 15 assay(s)
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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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Francis Crick InstituteUnited Kingdom10078

Revision History  (Full details and data files)

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