5M5G

Crystal structure of the Chaetomium Thermophilum polycomb repressive complex 2 (PRC2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5CH1


Literature

Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".

Zhang, Y.Justin, N.Wilson, J.R.Gamblin, S.J.

(2016) Science 354: 1543-1543

  • DOI: 10.1126/science.aaf6236
  • Primary Citation of Related Structures:  
    5M5G

  • PubMed Abstract: 
  • Jiao and Liu (Research Articles, 16 October 2015, aac4383) reported the crystal structure of the protein complex polycomb repressive complex 2 from Chaetomium thermophilum This landmark structure has brought invaluable insights into the activation mechanism of this essential methyltransferase ...

    Jiao and Liu (Research Articles, 16 October 2015, aac4383) reported the crystal structure of the protein complex polycomb repressive complex 2 from Chaetomium thermophilum This landmark structure has brought invaluable insights into the activation mechanism of this essential methyltransferase. However, the analysis of the x-ray data discussed below suggests that the description of oncogenic H3K27M peptide binding to the active site is incorrect.


    Related Citations: 
    • Structural Basis Of Histone H3K27 Trimethylation By An Active Polycomb Repressive Complex 2.
      Jiao, L., Liu, X.
      (2015) Science 350: C4383

    Organizational Affiliation

    Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. steve.gamblin@crick.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative polycomb protein EEDA605Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0029920
UniProt
Find proteins for G0S8H7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S8H7
Entity Groups  
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UniProt GroupG0S8H7
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinB937Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0053230
UniProt
Find proteins for G0SDW4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0SDW4
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UniProt GroupG0SDW4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3 11-Mer peptideC [auth D]11Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fragment from molecular 2 (region containing putative polycomb protein Suz12)D [auth E]9Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0006210
UniProt
Find proteins for G0RYC6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RYC6 
Go to UniProtKB:  G0RYC6
Entity Groups  
UniProt GroupG0RYC6
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C [auth D]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.554α = 90
b = 74.612β = 107.7
c = 128.508γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection