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- EMDB-23024: PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome -

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Entry
Database: EMDB / ID: EMD-23024
TitlePRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
Map dataPRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
Sample
  • Complex: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
    • Protein or peptide: Histone-lysine N-methyltransferase EZH1
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Polycomb protein SUZ12Polycomb-group proteins
    • Protein or peptide: Polycomb protein EED
  • Ligand: ZINC ION
KeywordsChromatin / methyltransferase / nucleosome-modifying complex / GENE REGULATION / GENE REGULATION-Transferase complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / histone H3K27 methyltransferase activity / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification ...[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / histone H3K27 methyltransferase activity / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / lncRNA binding / ATPase complex / G1/S-Specific Transcription / spinal cord development / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / subtelomeric heterochromatin formation / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / G0 and Early G1 / enzyme activator activity / anatomical structure morphogenesis / heterochromatin / heterochromatin formation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / methylated histone binding / Regulation of TP53 Activity through Acetylation / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / hippocampus development / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / chromosome / methylation / histone binding / Oxidative Stress Induced Senescence / cell population proliferation / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / nuclear body / chromatin remodeling / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
EZH1, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / 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, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / 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 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / 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 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SET domain superfamily / SET domain / SANT/Myb domain / SET domain profile. / SET domain / Zinc finger C2H2 type domain signature. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGrau DJ / Armache KJ
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
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  • Surface level: 0.007
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  • Surface view with fitted model
  • Atomic models: PDB-7ksr
  • Surface level: 0.007
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23024.png

Downloads & links

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Map

FileDownload / File: emd_23024.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.029805312 - 0.0433195
Average (Standard dev.)-0.000108560715 (±0.00093956623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z405.000405.000405.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0300.043-0.000

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Supplemental data

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Sample components

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Entire : PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome

EntireName: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
Components
  • Complex: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
    • Protein or peptide: Histone-lysine N-methyltransferase EZH1
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Polycomb protein SUZ12Polycomb-group proteins
    • Protein or peptide: Polycomb protein EED
  • Ligand: ZINC ION

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Supramolecule #1: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome

SupramoleculeName: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 266 KDa

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Macromolecule #1: Histone-lysine N-methyltransferase EZH1

MacromoleculeName: Histone-lysine N-methyltransferase EZH1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.394141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEIPNPPTSK CITYWKRKVK SEYMRLRQLK RLQANMGAKA LYVANFAKVQ EKTQILNEEW KKLRVQPVQS MKPVSGHPFL KKCTIESIF PGFASQHMLM RSLNTVALVP IMYSWSPLQQ NFMVEDETVL CNIPYMGDEV KEEDETFIEE LINNYDGKVH G EEEMIPGS ...String:
MEIPNPPTSK CITYWKRKVK SEYMRLRQLK RLQANMGAKA LYVANFAKVQ EKTQILNEEW KKLRVQPVQS MKPVSGHPFL KKCTIESIF PGFASQHMLM RSLNTVALVP IMYSWSPLQQ NFMVEDETVL CNIPYMGDEV KEEDETFIEE LINNYDGKVH G EEEMIPGS VLISDAVFLE LVDALNQYSD EEEEGHNDTS DGKQDDSKED LPVTRKRKRH AIEGNKKSSK KQFPNDMIFS AI ASMFPEN GVPDDMKERY RELTEMSDPN ALPPQCTPNI DGPNAKSVQR EQSLHSFHTL FCRRCFKYDC FLHPFHATPN VYK RKNKEI KIEPEPCGTD CFLLLEGAKE YAMLHNPRSK CSGRRRRRHH IVSASCSNAS ASAVAETKEG DSDRDTGNDW ASSS SEANS RCQTPTKQKA SPAPPQLCVV EAPSEPVEWT GAEESLFRVF HGTYFNNFCS IARLLGTKTC KQVFQFAVKE SLILK LPTD ELMNPSQKKK RKHRLWAAHC RKIQLKKDNS STQVYNYQPC DHPDRPCDST CPCIMTQNFC EKFCQCNPDC QNRFPG CRC KTQCNTKQCP CYLAVRECDP DLCLTCGASE HWDCKVVSCK NCSIQRGLKK HLLLAPSDVA GWGTFIKESV QKNEFIS EY CGELISQDEA DRRGKVYDKY MSSFLFNLNN DFVVDATRKG NKIRFANHSV NPNCYAKVVM VNGDHRIGIF AKRAIQAG E ELFFDYRYSQ ADALKYVGIE RETDVL

UniProtKB: Histone-lysine N-methyltransferase EZH1

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Macromolecule #2: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS

UniProtKB: Histone-binding protein RBBP4

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Macromolecule #3: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.181922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN ...String:
MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN DKPSPNSENE QNSVTLEVLL VKVCHKKRKD VSCPIRQVPT GKKQVPLNPD LNQTKPGNFP SLAVSSNEFE PS NSHMVKS YSLLFRVTRP GRREFNGMIN GETNENIDVN EELPARRKRN REDGEKTFVA QMTVFDKNRR LQLLDGEYEV AMQ EMEECP ISKKRATWET ILDGKRLPPF ETFSQGPTLQ FTLRWTGETN DKSTAPIAKP LATRNSESLH QENKPGSVKP TQTI AVKES LTTDLQTRKE KDTPNENRQK LRIFYQFLYN NNTRQQTEAR DDLHCPWCTL NCRKLYSLLK HLKLCHSRFI FNYVY HPKG ARIDVSINEC YDGSYAGNPQ DIHRQPGFAF SRNGPVKRTP ITHILVCRPK RTKASMSEFL ESEDGEVEQQ RTYSSG HNR LYFHSDTCLP LRPQEMEVDS EDEKDPEWLR EKTITQIEEF SDVNEGEKEV MKLWNLHVMK HGFIADNQMN HACMLFV EN YGQKIIKKNL CRNFMLHLVS MHDFNLISIM SIDKAVTKLR EMQQKLEKGE SASPANEEIT EEQNGTANGF SEINSKEK A LETDSVSGVS KQSKKQKL

UniProtKB: Polycomb protein SUZ12

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Macromolecule #4: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.267691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS ...String:
MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS RGIIRIINPI TMQCIKHYVG HGNAINELKF HPRDPNLLLS VSKDHALRLW NIQTDTLVAI FGGVEGHRDE VL SADYDLL GEKIMSCGMD HSLKLWRINS KRMMNAIKES YDYNPNKTNR PFISQKIHFP DFSTRDIHRN YVDCVRWLGD LIL SKSCEN AIVCWKPGKM EDDIDKIKPS ESNVTILGRF DYSQCDIWYM RFSMDFWQKM LALGNQVGKL YVWDLEVEDP HKAK CTTLT HHKCGAAIRQ TSFSRDSSIL IAVCDDASIW RWDRLR

UniProtKB: Polycomb protein EED

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES
50.0 mMsodium chlorideNaClSodium chloride
1.0 mMmagnesium chlorideMgCl2
1.0 mMdithiothreitol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3410000 / Details: Template based picking
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18151

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