9C8U

Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min

PDB DOI: https://doi.org/10.2210/pdb9C8U/pdb
EM Map EMD-43625: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-06-13 Released: 2024-09-04
Deposition Author(s): Abe, K.M., Li, G., He, Q., Grant, T., Lim, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min

Abe, K.M., Li, G., He, Q., Grant, T., Lim, C.

To be published.

Macromolecule Content

Total Structure Weight: 296.07 kDa
Atom Count: 12,252
Modelled Residue Count: 1,774
Deposited Residue Count: 2,606
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein SUZ12	A [auth B]	739	Homo sapiens	Mutation(s): 0 Gene Names: SUZ12, CHET9, JJAZ1, KIAA0160
UniProt & NIH Common Fund Data Resources
Find proteins for Q15022 (Homo sapiens) Explore Q15022 Go to UniProtKB: Q15022
PHAROS: Q15022 GTEx: ENSG00000178691
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15022
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	B [auth C]	367	Homo sapiens	Mutation(s): 0 Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens) Explore O75530 Go to UniProtKB: O75530
PHAROS: O75530 GTEx: ENSG00000074266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75530
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RBAP48	C [auth D]	425	Homo sapiens	Mutation(s): 0 Gene Names: RBBP4, RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens) Explore Q09028 Go to UniProtKB: Q09028
PHAROS: Q09028 GTEx: ENSG00000162521
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09028
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Histone-lysine N-methyltransferase EZH2	D [auth A]	750	Homo sapiens	Mutation(s): 0 Gene Names: EZH2, KMT6 EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens) Explore Q15910 Go to UniProtKB: Q15910
PHAROS: Q15910 GTEx: ENSG00000106462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15910
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Jumonji	E	31	Homo sapiens	Mutation(s): 0 Gene Names: JARID2, JMJ
UniProt & NIH Common Fund Data Resources
Find proteins for Q92833 (Homo sapiens) Explore Q92833 Go to UniProtKB: Q92833
PHAROS: Q92833 GTEx: ENSG00000008083
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92833
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein AEBP2	F	294	Homo sapiens	Mutation(s): 0 Gene Names: AEBP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZN18 (Homo sapiens) Explore Q6ZN18 Go to UniProtKB: Q6ZN18
PHAROS: Q6ZN18 GTEx: ENSG00000139154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZN18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM130550
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00GM131023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM150023