[English] 日本語
Yorodumi
- PDB-9dch: Single-stranded RNA-mediated PRC2 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dch
TitleSingle-stranded RNA-mediated PRC2 dimer
Components
  • (Polycomb protein ...) x 2
  • Isoform 2 of Histone-lysine N-methyltransferase EZH2
  • Protein Jumonji
  • RBAP48
  • TERRAmut RNA
  • Zinc finger protein AEBP2
KeywordsGENE REGULATION / PRC2 / RNA / RNP complex / chromatin modifier
Function / homology
Function and homology information


regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / RSC-type complex / ubiquitin-modified histone reader activity / sex chromatin ...regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / RSC-type complex / ubiquitin-modified histone reader activity / sex chromatin / positive regulation of cell cycle G1/S phase transition / NURF complex / regulatory ncRNA-mediated heterochromatin formation / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / regulation of stem cell differentiation / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / pronucleus / positive regulation of dendrite development / histone H3K9me2/3 reader activity / positive regulation of protein serine/threonine kinase activity / histone H3 methyltransferase activity / spinal cord development / histone methyltransferase activity / synaptic transmission, GABAergic / Sin3-type complex / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of MAP kinase activity / positive regulation of stem cell population maintenance / histone deacetylase complex / lncRNA binding / histone methyltransferase complex / Transcriptional Regulation by E2F6 / negative regulation of cell differentiation / RNA Polymerase I Transcription Initiation / G0 and Early G1 / subtelomeric heterochromatin formation / positive regulation of GTPase activity / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / Cyclin E associated events during G1/S transition / pericentric heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / RNA polymerase II core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / B cell differentiation / nucleosome binding / stem cell differentiation / heterochromatin / negative regulation of cytokine production involved in inflammatory response / negative regulation of cell migration / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of transforming growth factor beta receptor signaling pathway / hippocampus development / Regulation of PTEN gene transcription / transcription corepressor binding / SUMOylation of chromatin organization proteins / central nervous system development / brain development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / ubiquitin binding / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / protein-DNA complex / chromatin DNA binding / Negative Regulation of CDH1 Gene Transcription / PKMTs methylate histone lysines / regulation of circadian rhythm / Activation of anterior HOX genes in hindbrain development during early embryogenesis / enzyme activator activity / histone deacetylase binding / transcription coregulator activity / HCMV Early Events / rhythmic process / transcription corepressor activity / regulation of gene expression / response to estradiol / Regulation of PD-L1(CD274) transcription / nucleosome assembly / methylation / chromosome / heterochromatin formation / histone binding / Oxidative Stress Induced Senescence / chromatin organization / Potential therapeutics for SARS
Similarity search - Function
: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain ...: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / : / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
RNA / Polycomb protein EED / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Zinc finger protein AEBP2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSong, J.S. / Kasinath, V.K.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM132544 United States
CitationJournal: bioRxiv / Year: 2025
Title: RNA-induced PRC2 inhibition depends on the sequence of bound RNA.
Authors: Jiarui Song / Liqi Yao / Anne R Gooding / Valentin Thron / Wayne O Hemphill / Karen Goodrich / Vignesh Kasinath / Thomas R Cech
Abstract: Methyltransferase PRC2 (Polycomb Repressive Complex 2) deposits histone H3K27 trimethylation to establish and maintain epigenetic gene silencing. PRC2 is precisely regulated by accessory proteins, ...Methyltransferase PRC2 (Polycomb Repressive Complex 2) deposits histone H3K27 trimethylation to establish and maintain epigenetic gene silencing. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications and, particularly, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells, a mechanism explained by our recent cryo-EM structure showing G4 RNA-mediated PRC2 dimerization. However, PRC2 binds a wide variety of RNA sequences, and it remains unclear how diverse RNAs beyond G4 associate with and regulate PRC2. Here, we show that variations in RNA sequence elicit distinct effects on PRC2 function. A single-stranded G-rich RNA and an atypical G4 structure called a pUG-fold mediate PRC2 dimerization nearly identical to that induced by G4 RNA. In contrast, pyrimidine-rich RNAs, including a motif identified by CLIPseq in cells, do not induce PRC2 dimerization and instead bind PRC2 monomers with retention of methyltransferase activity. Only RNAs that dimerize PRC2 compete with nucleosome binding and inhibit PRC2 methyltransferase activity. CRISPR-dCas9 was adapted to localize different RNA elements onto a PRC2-targeted gene, revealing RNA sequence specificity for PRC2 regulation in cells. Thus, PRC2 binds many different RNAs with similar affinity, however, the functional effect on enzymatic activity depends entirely on the sequence of the bound RNA, a conclusion potentially applicable to any RNA- binding protein with a large transcriptome.
History
DepositionAug 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: TERRAmut RNA
A: Isoform 2 of Histone-lysine N-methyltransferase EZH2
B: Polycomb protein SUZ12
D: RBAP48
F: Zinc finger protein AEBP2
E: Protein Jumonji
C: Polycomb protein EED
H: Isoform 2 of Histone-lysine N-methyltransferase EZH2
I: Polycomb protein SUZ12
K: RBAP48
M: Zinc finger protein AEBP2
L: Protein Jumonji
J: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)674,67627
Polymers673,76013
Non-polymers91614
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 4 types, 8 molecules AHDKFMEL

#2: Protein Isoform 2 of Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 86017.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q15910, [histone H3]-lysine27 N-trimethyltransferase
#4: Protein RBAP48 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I 48 kDa subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09028
#5: Protein Zinc finger protein AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 32881.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZN18
#6: Protein Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 36021.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92833

-
Polycomb protein ... , 2 types, 4 molecules BICJ

#3: Protein Polycomb protein SUZ12 / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 82353.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15022
#7: Protein Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 50267.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75530

-
RNA chain / Non-polymers , 2 types, 15 molecules G

#1: RNA chain TERRAmut RNA


Mass: 3257.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Single-stranded RNA-mediated dimer of Polycomb Repressive Complex 2COMPLEX#1-#70MULTIPLE SOURCES
2dimer of Polycomb Repressive Complex 2COMPLEX#2-#71RECOMBINANT
3TERRAmut RNACOMPLEX#11SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: BTI-Tn-5B1-4
Buffer solutionpH: 7.9
Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1 mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1 mM TCEP) EM ...Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1 mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1 mM TCEP) EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1 mM TCEP).
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: We used streptavidin-affinity grid preparation method with biotin-labeled RNA at 100 nM concentration. PRC2 was applied in excess at 600 nM.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 K / Details: 2-3s of single side blotting

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 130000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 14230
Details: Cryo-EM data was collected using a Titan Krios G3i equipped with a Thermo Fisher Falcon 4 direct-electron detector (DED) camera and a Selectris energy filter set with a 10-eV slit width. ...Details: Cryo-EM data was collected using a Titan Krios G3i equipped with a Thermo Fisher Falcon 4 direct-electron detector (DED) camera and a Selectris energy filter set with a 10-eV slit width. Data acquisition was performed using Thermo Fisher EPU at 130,000x magnification (0.97 A/pixel) with a defocus range of minus 1.9 to minus 0.5 micrometer. Movies were collected in EER format with a total dose of 50 electrons per square angstrom and an exposure time of 5.49 s corresponding to 1323 frames.
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2EPUimage acquisition
4RELION5CTF correction
7Cootmodel fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13PHENIXmodel refinement
Image processingDetails: Gain correction was applied during motion correction using Relion own implementation of the UCSF motioncor2 program
CTF correctionDetails: CTFind / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3385491 / Details: TOPAZ auto picking
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120658 / Symmetry type: POINT
Atomic model buildingDetails: Individual PRC2 protomers were built using cryo-EM maps from the multibody refinement. The coordinates of G-quadruplex RNA-bound PRC2 six-subunit complex (PDB: 8FYH) provided a starting ...Details: Individual PRC2 protomers were built using cryo-EM maps from the multibody refinement. The coordinates of G-quadruplex RNA-bound PRC2 six-subunit complex (PDB: 8FYH) provided a starting model from which all the coordinates were adjusted and rebuilt in the new map using COOT. The model of each PRC2 promoter was subjected to global refinement and minimization in real space using PHENIX. These were then subjected to manual inspection and adjustment in COOT, followed by refinement again in PHENIX. TERRAmut RNA model was generated using a 10-nucleotide single-stranded fragment (UGAGUGUGAG) using AlphaFold3 and then docked into our map for the position we designated as the RNA density.
Atomic model buildingPDB-ID: 8FYH

8fyh


Accession code: 8FYH / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more