5KKL

Structure of ctPRC2 in complex with H3K27me3 and H3K27M

PDB DOI: https://doi.org/10.2210/pdb5KKL/pdb

Classification: TRANSFERASE
Organism(s): Thermochaetoides thermophila DSM 1495, Homo sapiens
Expression System: Saccharomyces cerevisiae S288C
Mutation(s): Yes

Deposited: 2016-06-21 Released: 2017-04-19
Deposition Author(s): Jiao, L., Liu, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.234
R-Value Work: 0.186
R-Value Observed: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

Jiao, L., Liu, X.

(2016) Science 354: 1543-1543

PubMed: 28008038 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.aaj2335
Primary Citation of Related Structures:
5KJH, 5KJI, 5KKL

PubMed Abstract:
Zhang et al suggested that in the crystal structure of a polycomb repressive complex 2 from Chaetomium thermophilum (ctPRC2), a flexible linker region, but not the H3K27M cancer mutant peptide, better fits the electron density. Based on our new data, we agree with this alternative interpretation and provide the crystal structure of ctPRC2 bound to a bona fide H3K27M sequence.

Organizational Affiliation

Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecule Content

Total Structure Weight: 174.98 kDa
Atom Count: 10,614
Modelled Residue Count: 1,328
Deposited Residue Count: 1,554
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein,Histone H3.1 peptide,Zinc finger domain-containing protein	B	938	Thermochaetoides thermophila DSM 1495, Homo sapiens	Mutation(s): 1 Gene Names: CTHT_0053230 EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for G0RYC6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RYC6 Go to UniProtKB: G0RYC6
Find proteins for G0SDW4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SDW4 Go to UniProtKB: G0SDW4
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 Groups	G0RYC6G0SDW4P68431
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth B] 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] MOL2 format, chain D [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] mmCIF format, chain D [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]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] 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]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.234
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.254	α = 90
b = 80.559	β = 107.42
c = 133.22	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

Jiao, L.

Liu, X.

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2017-08-23
Changes: Data collection
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description