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- PDB-7ksr: PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome -

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Basic information

Entry
Database: PDB / ID: 7ksr
TitlePRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
Components
  • Histone-binding protein RBBP4
  • Histone-lysine N-methyltransferase EZH1
  • Polycomb protein EED
  • Polycomb protein SUZ12
KeywordsGENE REGULATION/Transferase / Chromatin / methyltransferase / nucleosome-modifying complex / GENE REGULATION / GENE REGULATION-Transferase complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / regulation of adaxial/abaxial pattern formation / histone H3K27 methyltransferase activity / sex chromatin / NURF complex / facultative heterochromatin formation / NuRD complex ...[histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / regulation of adaxial/abaxial pattern formation / histone H3K27 methyltransferase activity / sex chromatin / NURF complex / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / genomic imprinting / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / RSC-type complex / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / chromatin silencing complex / histone H3K9me2/3 reader activity / Transcription of E2F targets under negative control by DREAM complex / pronucleus / spinal cord development / ATPase complex / lncRNA binding / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / : / positive regulation of stem cell population maintenance / oligodendrocyte differentiation / histone deacetylase complex / RNA Polymerase I Transcription Initiation / G0 and Early G1 / negative regulation of cell differentiation / anatomical structure morphogenesis / subtelomeric heterochromatin formation / heterochromatin / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / SUMOylation of chromatin organization proteins / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / hippocampus development / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / promoter-specific chromatin binding / molecular condensate scaffold activity / negative regulation of transforming growth factor beta receptor signaling pathway / protein-DNA complex / brain development / chromatin DNA binding / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / heterochromatin formation / nucleosome assembly / histone binding / Oxidative Stress Induced Senescence / methylation / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / cell population proliferation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
EZH1, SET domain / Polycomb protein SUZ12-like, Zn 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 ...EZH1, SET domain / Polycomb protein SUZ12-like, Zn 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 / : / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Zinc finger C2H2 type domain signature. / 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
Polycomb protein EED / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGrau, D.J. / Armache, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115882 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction.
Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas ...Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas Walz / Karim-Jean Armache /
Abstract: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the ...Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EZH1
D: Histone-binding protein RBBP4
C: Polycomb protein SUZ12
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,01111
Polymers266,5534
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Histone-lysine N-methyltransferase EZH1 / ENX-2 / Enhancer of zeste homolog 1


Mass: 85394.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH1, KIAA0388 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92800, [histone H3]-lysine27 N-trimethyltransferase
#2: Protein Histone-binding protein RBBP4 / 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 p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#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: 83181.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022
#4: 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75530
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: .266 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
250 mMsodium chlorideNaCl1
31 mMmagnesium chlorideMgCl21
41 mMdithiothreitol1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 56.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: CTF correction
CTF correctionDetails: Patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3410000 / Details: Template based picking
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18151 / Symmetry type: POINT

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