+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29647 | |||||||||
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Title | Body1 of G4 RNA-mediated PRC2 dimer from multibody refinement | |||||||||
Map data | ||||||||||
Sample |
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Keywords | PRC2 / G-quadruplex RNA / RNP complex / chromatin modifier / GENE REGULATION | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Jiarui JS / Vignesh VK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Science / Year: 2023 Title: Structural basis for inactivation of PRC2 by G-quadruplex RNA. Authors: Jiarui Song / Anne R Gooding / Wayne O Hemphill / Brittney D Love / Anne Robertson / Liqi Yao / Leonard I Zon / Trista E North / Vignesh Kasinath / Thomas R Cech / 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 ...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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29647.map.gz | 57.9 MB | EMDB map data format | |
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Header (meta data) | emd-29647-v30.xml emd-29647.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29647_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_29647.png | 79.6 KB | ||
Masks | emd_29647_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-29647.cif.gz | 8.4 KB | ||
Others | emd_29647_additional_1.map.gz emd_29647_half_map_1.map.gz emd_29647_half_map_2.map.gz | 9.9 MB 58.3 MB 58.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29647 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29647 | HTTPS FTP |
-Validation report
Summary document | emd_29647_validation.pdf.gz | 797.7 KB | Display | EMDB validaton report |
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Full document | emd_29647_full_validation.pdf.gz | 797.2 KB | Display | |
Data in XML | emd_29647_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_29647_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29647 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29647 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29647.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06344 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29647_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_29647_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29647_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29647_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : G4 RNA-mediated dimer of polycomb repressive complex 2
Entire | Name: G4 RNA-mediated dimer of polycomb repressive complex 2 |
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Components |
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-Supramolecule #1: G4 RNA-mediated dimer of polycomb repressive complex 2
Supramolecule | Name: G4 RNA-mediated dimer of polycomb repressive complex 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Polycomb protein SUZ12
Macromolecule | Name: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Polycomb protein EED
Macromolecule | Name: Polycomb protein EED / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Histone-binding protein RBBP4
Macromolecule | Name: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: Histone-lysine N-methyltransferase EZH2
Macromolecule | Name: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND ...String: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND EIFVELVNAL GQYNDDDDDD DGDDPEEREE KQKDLEDHRD DKESRPPRKF PSDKIFEAIS SMFPDKGTAE EL KEKYKEL TEQQLPGALP PECTPNIDGP NAKSVQREQS LHSFHTLFCR RCFKYDCFLH RKCNYSFHAT PNTYKRKNTE TAL DNKPCG PQCYQHLEGA KEFAAALTAE RIKTPPKRPG GRRRGRLPNN SSRPSTPTIN VLESKDTDSD REAGTETGGE NNDK EEEEK KDETSSSSEA NSRCQTPIKM KPNIEPPENV EWSGAEASMF RVLIGTYYDN FCAIARLIGT KTCRQVYEFR VKESS IIAP APAEDVDTPP RKKKRKHRLW AAHCRKIQLK KDGSSNHVYN YQPCDHPRQP CDSSCPCVIA QNFCEKFCQC SSECQN RFP GCRCKAQCNT KQCPCYLAVR ECDPDLCLTC GAADHWDSKN VSCKNCSIQR GSKKHLLLAP SDVAGWGIFI KDPVQKN EF ISEYCGEIIS QDEADRRGKV YDKYMCSFLF NLNNDFVVDA TRKGNKIRFA NHSVNPNCYA KVMMVNGDHR IGIFAKRA I QTGEELFFDY RYSQADALKY VGIEREMEIP |
-Macromolecule #5: protein Jumonji isoform X3
Macromolecule | Name: protein Jumonji isoform X3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNAQKRQHGE GIAGSLKSVN GLLGNDQSKA LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKTVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA ...String: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNAQKRQHGE GIAGSLKSVN GLLGNDQSKA LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKTVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA LPSSMVYFGS SQDEEDVEEE DDETEDVKTA NNNASSSCQS TPRKGKTHKH VHNGHVFNGS NRSTREKEPA QK HKSKETT PAKEKHIDHR ADSRREPASV AQPTATPSAG SLAKGLPANH QPPPPHRSAQ DLRKQVTLHV SKVNGVTRMS SLG AGTTSA KKIREVRPSP SKTVKYTATV TKGTVTYTKA KRELVKETKP THHKPSSAVN HTISGKTESS NAKTRKQVLS LGGA STSTG PAASGLKASS RLNPKSCTKE VGGRQLREGL RNSKRRLEEA QQVDKPQSPP KKMKGAAGIA EAPGKKASAA SAEKS LLNG HVKKEVPERS LERNRPKRAT AGKNMPGKQA HGKAEGTPCE NRSTSQPESS HKPHDPQGKP EKGIGKSGWT AMDEIP VLR PSAKEFHDPL IYIESVRAQV EKYGMCRVIP PPDWRPECKL NDEMRFVTQI QHIHKLGRRW GPNVQRLACI KKHLRSQ GI TMDELPLIGG CELDLACFFR LINEMGGMQQ VTDLKKWNKL ADMLRIPKTA QDRLAKLQEA YCQYLLSYDS LSPEEHRR L EKEVLMEKEI LEKRKGPLEG HTENDHHKFH SLPRFEPKNG LIHGVTPRNG FRSKLKEVGQ APLKTGRRRL FAQEKEVVK EEEEDKGVLN DFHKCIYKGR SVSLTTFYRT ARNIMNMCFS KEPAPAEIEQ EYWRLVEEKD CHVAVHCGKV DTNTHGSGFP VGKSEPFSR HGWNLTVLPN NTGSILRHLG AVPGVTIPWL NIGMVFSTSC WSRDQNHLPY IDYLHTGADC IWYCIPAEEE N KLEDVVHT LLQANGTPGL QMLESNVMIS PEVLCKEGIK VHRTVQQSGQ FVVCFPGSFV SKVCCGYSVS ETVHFATTQW TS MGFETAK EMKRRHIAKP FSMEKLLYQI AQAEAKKENG PTLSTISALL DELRDTELRQ RRQLFEAGLH SSARYGSHDG NST VADGKK KPRKWLQLET SERRCQICQH LCYLSMVVQE NENVVFCLEC ALRHVEKQKS CRGLKLMYRY DEEQIISLVN QICG KVSGK HGGIENCLNK PTPKRGPRKR ATVDVPPSRL PSS |
-Macromolecule #6: Zinc finger protein AEBP2
Macromolecule | Name: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MAAAITDMAD LEELSRLSPL PPGSPGSAAR GRAEPPEEEE EEEEEEEEAE AEAVAALLLN GGSGGGGGGG GGGVGGGEAE TMSEPSPES ASQAGEDEDE EEDDEEEEDE SSSSGGGEEE SSAESLVGSS GGSSSDETRS LSPGAASSSS GDGDGKEGLE E PKGPRGSQ ...String: MAAAITDMAD LEELSRLSPL PPGSPGSAAR GRAEPPEEEE EEEEEEEEAE AEAVAALLLN GGSGGGGGGG GGGVGGGEAE TMSEPSPES ASQAGEDEDE EEDDEEEEDE SSSSGGGEEE SSAESLVGSS GGSSSDETRS LSPGAASSSS GDGDGKEGLE E PKGPRGSQ GGGGGGSSSS SVVSSGGDEG YGTGGGGSSA TSGGRRGSLE MSSDGEPLSR MDSEDSISST IMDVDSTISS GR STPAMMN GQGSTTSSSK NIAYNCCWDQ CQACFNSSPD LADHIRSIHV DGQRGGVFVC LWKGCKVYNT PSTSQSWLQR HML THSGDK PFKCVVGGCN ASFASQGGLA RHVPTHFSQQ NSSKVSSQPK AKEESPSKAG MNKRRKLKNK RRRSLPRPHD FFDA QTLDA IRHRAICFNL SAHIESLGKG HSVVFHSTVI AKRKEDSGKI KLLLHWMPED ILPDVWVNES ERHQLKTKVV HLSKL PKDT ALLLDPNIYR TMPQKRLKRT LIRKVFNLYL SKQ |
-Macromolecule #7: G4 RNA
Macromolecule | Name: G4 RNA / type: rna / ID: 7 |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: GGGUAAGGGU AAGGGUAAGG GUAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1mM TCEP) EM preparation ...Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1mM TCEP) EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1mM TCEP). |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA PLUNGER / Details: 3s of single side blotting. |
Details | We used streptavidin-affinity grid preparation method with biotin-labeled RNA at 100 nM concentration. PRC2 was applied in excess at 600 nM. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 18632 / Average electron dose: 60.0 e/Å2 / Details: 60 frames per movie |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |