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- EMDB-23022: Cryo-EM map of PRC2:EZH1-AEBP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-23022
TitleCryo-EM map of PRC2:EZH1-AEBP2
Map dataCryo-EM map of PRC2:EZH1-AEBP2
Sample
  • Complex: PRC2:EZH1-AEBP2
    • Protein or peptide: EZH1
    • Protein or peptide: EED
    • Protein or peptide: SUZ12
    • Protein or peptide: RBAP48RBBP4
    • Protein or peptide: AEBP2
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation ...protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / 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 / cardiac muscle cell proliferation / histone methyltransferase complex / 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 / spleen development / methylated histone binding / Regulation of TP53 Activity through Acetylation / cellular response to leukemia inhibitory factor / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / thymus development / liver development / PRC2 methylates histones and DNA / ubiquitin binding / Regulation of PTEN gene transcription / central nervous system development / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / stem cell differentiation / hippocampus development / transcription coregulator activity / 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 / chromatin organization / methylation / histone binding / regulation of gene expression / 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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II
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 / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / 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 / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / 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 / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Zinc finger protein AEBP2 / Histone-lysine N-methyltransferase EZH1 / Protein Jumonji
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 23, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23022.png

Downloads & links

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Map

FileDownload / File: emd_23022.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of PRC2:EZH1-AEBP2
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.16578752 - 0.2602548
Average (Standard dev.)0.00037932236 (±0.010198578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z234.000234.000234.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1660.2600.000

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Supplemental data

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Sample components

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Entire : PRC2:EZH1-AEBP2

EntireName: PRC2:EZH1-AEBP2
Components
  • Complex: PRC2:EZH1-AEBP2
    • Protein or peptide: EZH1
    • Protein or peptide: EED
    • Protein or peptide: SUZ12
    • Protein or peptide: RBAP48RBBP4
    • Protein or peptide: AEBP2

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Supramolecule #1: PRC2:EZH1-AEBP2

SupramoleculeName: PRC2:EZH1-AEBP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 299 KDa

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Macromolecule #1: EZH1

MacromoleculeName: EZH1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd ...String:
meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd gkvhg eeem ipgsvl isd avflelv da lnqysdee e eghndtsdg kqddskedlp vtrkrkrha i egnkkssk kq fpndmif sai asmfpe ngvp ddmke ryrel tems dpnalp pqc tpnidgp na ksvqreqs l hsfhtlfcr rcfkydcflh pfhatpnvy k rknkeiki ep epcgtdc fll legake yaml hnprs kcsgr rrrr hhivsa scs nasasav ae tkegdsdr d tgndwasss seansrcqtp tkqkaspap p qlcvveap se pvewtga ees lfrvfh gtyf nnfcs iarll gtkt ckqvfq fav keslilk lp tdelmnps q kkkrkhrlw aahcrkiqlk kdnsstqvy n yqpcdhpd rp cdstcpc imt qnfcek fcqc npdcq nrfpg crck tqcntk qcp cylavre cd pdlcltcg a sehwdckvv sckncsiqrg lkkhlllap s dvagwgtf ik esvqkne fis eycgel isqd eadrr gkvyd kyms sflfnl nnd fvvdatr kg nkirfanh s vnpncyakv vmvngdhrig ifakraiqa g eelffdyr ys qadalky vgi eretdv l

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Macromolecule #2: EED

MacromoleculeName: EED / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd ...String:
mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd sntsh plla vagsrg iir iinpitm qc ikhyvghg n ainelkfhp rdpnlllsvs kdhalrlwn i qtdtlvai fg gveghrd evl sadydl lgek imscg mdhsl klwr inskrm mna ikesydy np nktnrpfi s qkihfpdfs trdihrnyvd cvrwlgdli l skscenai vc wkpgkme ddi dkikps esnv tilgr fdysq cdiw ymrfsm dfw qkmlalg nq vgklyvwd l evedphkak cttlthhkcg aairqtsfs r dssiliav cd dasiwrw drl r

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Macromolecule #3: SUZ12

MacromoleculeName: SUZ12 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa ...String:
mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa hlqlt ftgf fhkndk psp nseneqn sv tlevllvk v chkkrkdvs cpirqvptgk kqvplnpdl n qtkpgnfp sl avssnef eps nshmvk sysl lfrvt rpgrr efng minget nen idvneel pa rrkrnred g ektfvaqmt vfdknrrlql ldgeyevam q emeecpis kk ratweti ldg krlppf etfs qgptl qftlr wtge tndkst api akplatr ns eslhqenk p gsvkptqti avkeslttdl qtrkekdtp n enrqklri fy qflynnn trq qteard dlhc pwctl ncrkl ysll khlklc hsr fifnyvy hp kgaridvs i necydgsya gnpqdihrqp gfafsrngp v krtpithi lv crpkrtk asm sefles edge veqqr tyssg hnrl yfhsdt clp lrpqeme vd sedekdpe w lrektitqi eefsdvnege kevmklwnl h vmkhgfia dn qmnhacm lfv enygqk iikk nlcrn fmlhl vsmh dfnlis ims idkavtk lr emqqklek g esaspanee iteeqngtan gfseinske k aletdsvs gv skqskkq kl

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Macromolecule #4: RBAP48

MacromoleculeName: RBAP48 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt ...String:
madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt khpsk pdps gecnpd lrl rghqkeg yg lswnpnls g hllsasddh ticlwdisav pkegkvvda k tiftghta vv edvswhl lhe slfgsv addq klmiw dtrsn ntsk pshsvd aht aevncls fn pysefila t gsadktval wdlrnlklkl hsfeshkde i fqvqwsph ne tilassg tdr rlnvwd lski geeqs pedae dgpp ellfih ggh takisdf sw npnepwvi c svsednimq vwqmaeniyn dedpegsvd p egqgs

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Macromolecule #5: AEBP2

MacromoleculeName: AEBP2 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss ...String:
mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss qpkak eesp skagmn krr klknkrr rs lprphdff d aqtldairh raicfnlsah ieslgkghs v vfhstvia kr kedsgki kll lhwmpe dilp dvwvn eserh qlkt kvvhls klp kdtalll dp niyrtmpq k rlkr

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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

Concentration0.05 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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3142334
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155809

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