8FYH | pdb_00008fyh

G4 RNA-mediated PRC2 dimer

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2023-01-26 Released: 2023-10-04 
  • Deposition Author(s): Song, J., Kasinath, V.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8FYH

This is version 1.1 of the entry. See complete history

Literature

Structural basis for inactivation of PRC2 by G-quadruplex RNA.

Song, J.Gooding, A.R.Hemphill, W.O.Love, B.D.Robertson, A.Yao, L.Zon, L.I.North, T.E.Kasinath, V.Cech, T.R.

(2023) Science 381: 1331-1337

  • DOI: https://doi.org/10.1126/science.adh0059
  • Primary Citation Related Structures: 
    8FYH

  • PubMed Abstract: 

    Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. PRC2 associates with numerous precursor messenger RNAs (pre-mRNAs) and long noncoding RNAs (lncRNAs) with a binding preference for G-quadruplex RNA. In this work, we present a 3.3-Å-resolution cryo-electron microscopy structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface composed of two copies of the catalytic subunit EZH2, thereby blocking nucleosome DNA interaction and histone H3 tail accessibility. Furthermore, an RNA-binding loop of EZH2 facilitates the handoff between RNA and DNA, another activity implicated in PRC2 regulation by RNA. We identified a gain-of-function mutation in this loop that activates PRC2 in zebrafish. Our results reveal mechanisms for RNA-mediated regulation of a chromatin-modifying enzyme.


  • Organizational Affiliation
    • Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.

Macromolecule Content 

  • Total Structure Weight: 929.37 kDa 
  • Atom Count: 25,638 
  • Modeled Residue Count: 3,710 
  • Deposited Residue Count: 8,246 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12A [auth B],
G [auth H]
739Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15022
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polycomb protein EEDB [auth C],
H [auth I]
441Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75530
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4C [auth D],
I [auth J]
425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09028
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2D [auth A],
J [auth G]
751Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15910
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
protein Jumonji isoform X3
E, K
1,238Homo sapiensMutation(s): 0 
Gene Names: Jarid2
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger protein AEBP2
F, L
517Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZN18
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 7
MoleculeChains LengthOrganismImage
G4 RNA24Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth G]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
AA [auth G],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth G],
V [auth G],
W [auth G],
X [auth G],
Y [auth G],
Z [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0-beta-2
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM132544

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary