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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 28008037 Search on PubMed
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S8H7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 EC: 2.1.1.356
UniProt
Find proteins for G0SDW4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SDW4 Go to UniProtKB: G0SDW4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0SDW4
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
UniProt Group	G0RYC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain M [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth B] 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		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]