5M5G

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

• PDB DOI: https://doi.org/10.2210/pdb5M5G/pdb

• Classification: TRANSFERASE
• Organism(s): Thermochaetoides thermophila DSM 1495, Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2016-10-21 Released: 2017-01-11 
• Deposition Author(s): Zhang, Y., Justin, N., Wilson, J., Gamblin, S.

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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 

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

• PubMed: 28008037 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.87 kDa 
• Atom Count: 10,893 
• Modelled Residue Count: 1,295 
• Deposited Residue Count: 1,562 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative polycomb protein EED	A	605	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0029920
UniProt
Find proteins for G0S8H7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S8H7  Go to UniProtKB:  G0S8H7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	B	937	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0053230
UniProt
Find proteins for G0SDW4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SDW4  Go to UniProtKB:  G0SDW4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3 11-Mer peptide	C [auth D]	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragment from molecular 2 (region containing putative polycomb protein Suz12)	D [auth E]	9	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0RYC6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RYC6  Go to UniProtKB:  G0RYC6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	M [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	C [auth D]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

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 = 81.554	α = 90
b = 74.612	β = 107.7
c = 128.508	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Zhang, Y., Justin, N., Wilson, J., Gamblin, S.

Revision History  

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