8FYH

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


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 of 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.


Macromolecules

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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)
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PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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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)
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PHAROS:  O75530
GTEx:  ENSG00000074266 
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UniProt GroupO75530
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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)
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PHAROS:  Q09028
GTEx:  ENSG00000162521 
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UniProt GroupQ09028
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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)
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PHAROS:  Q15910
GTEx:  ENSG00000106462 
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UniProt GroupQ15910
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
protein Jumonji isoform X3
E, K
1,238Homo sapiensMutation(s): 0 
Gene Names: Jarid2
UniProt
Find proteins for A0A6I9KXB3 (Peromyscus maniculatus bairdii)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein AEBP2
F, L
517Homo sapiensMutation(s): 0 
Gene Names: AEBP2
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Find proteins for Q6ZN18 (Homo sapiens)
Explore Q6ZN18 
Go to UniProtKB:  Q6ZN18
PHAROS:  Q6ZN18
GTEx:  ENSG00000139154 
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UniProt GroupQ6ZN18
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  • Reference Sequence

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Entity ID: 7
MoleculeChains LengthOrganismImage
G4 RNA24Homo sapiens
Sequence Annotations
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  • 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