2024-10-30 REL RCSB RCSB RCSB 2023-01-26 2023-10-04 2023-10-04 2024-10-30 Howard Hughes Medical Institute (HHMI) United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R00GM132544 United States G4 RNA-mediated PRC2 dimer Song J Kasinath V PRC2, G-quadruplex RNA, RNP complex, chromatin modifier, GENE REGULATION Song J Gooding AR Hemphill WO Love BD Robertson A Yao L Zon LI North TE Kasinath V Cech TR Structural basis for inactivation of PRC2 by G-quadruplex RNA. Science US 381 1331 1337 2023 37733873 doi:10.1126/science.adh0059 1095-9203 0038 SCIEAS EMD-29647 other EM volume
Body1 of G4 RNA-mediated PRC2 dimer from multibody refinement
 EMD-29656 other EM volume
Body2 of G4 RNA-mediated PRC2 dimer from multibody refinement
 8fyh FULLOVERLAP G4 RNA-mediated dimer of polycomb repressive complex 2 G4 RNA-mediated dimer of polycomb repressive complex 2 0 1 2 3 4 5 6 7 Homo sapiens 0.8 Polycomb protein SUZ12 Homo sapiens 0.083181922 2 Trichoplusia ni LEVO MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQ ADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLT FTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQ EMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTI AVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVEQQRTYSSG HNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFV ENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK ALETDSVSGVSKQSKKQKL Q15022 Polycomb protein EED Homo sapiens 0.050267690999999996 2 Trichoplusia ni LEVO MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTPNAPGRKSWGKGKWKSKKCKY SFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSH PLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLIL SKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAK CTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR O75530 Histone-binding protein RBBP4 Homo sapiens 0.047709527 2 Trichoplusia ni LEVO MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLV IASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSK PDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEI FQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQ VWQMAENIYNDEDPEGSVDPEGQGS Q09028 Histone-lysine N-methyltransferase EZH2 Homo sapiens 0.08614905499999999 2 Trichoplusia ni LEVO MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWKQRRIQPVHILTSVSSLRGT RECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGD RECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKCNYSFHATPNTYKRKNTETAL DNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDK EEEEKKDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESS IIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQN RFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKN EFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRA IQTGEELFFDYRYSQADALKYVGIEREMEIP Q15910 2.1.1.356 protein Jumonji isoform X3 Homo sapiens 0.138406219 2 Trichoplusia ni LEVO MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNAQKRQHGEGIAGSLKSVNGLLGNDQSKALGPASEQSEN EKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQSQPNSPSTTPVKTVEPLLPPPATQISDLSKRKPKTEDFLTF LCLRGSPALPSSMVYFGSSQDEEDVEEEDDETEDVKTANNNASSSCQSTPRKGKTHKHVHNGHVFNGSNRSTREKEPAQK HKSKETTPAKEKHIDHRADSRREPASVAQPTATPSAGSLAKGLPANHQPPPPHRSAQDLRKQVTLHVSKVNGVTRMSSLG AGTTSAKKIREVRPSPSKTVKYTATVTKGTVTYTKAKRELVKETKPTHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGA STSTGPAASGLKASSRLNPKSCTKEVGGRQLREGLRNSKRRLEEAQQVDKPQSPPKKMKGAAGIAEAPGKKASAASAEKS LLNGHVKKEVPERSLERNRPKRATAGKNMPGKQAHGKAEGTPCENRSTSQPESSHKPHDPQGKPEKGIGKSGWTAMDEIP VLRPSAKEFHDPLIYIESVRAQVEKYGMCRVIPPPDWRPECKLNDEMRFVTQIQHIHKLGRRWGPNVQRLACIKKHLRSQ GITMDELPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQYLLSYDSLSPEEHRR LEKEVLMEKEILEKRKGPLEGHTENDHHKFHSLPRFEPKNGLIHGVTPRNGFRSKLKEVGQAPLKTGRRRLFAQEKEVVK EEEEDKGVLNDFHKCIYKGRSVSLTTFYRTARNIMNMCFSKEPAPAEIEQEYWRLVEEKDCHVAVHCGKVDTNTHGSGFP VGKSEPFSRHGWNLTVLPNNTGSILRHLGAVPGVTIPWLNIGMVFSTSCWSRDQNHLPYIDYLHTGADCIWYCIPAEEEN KLEDVVHTLLQANGTPGLQMLESNVMISPEVLCKEGIKVHRTVQQSGQFVVCFPGSFVSKVCCGYSVSETVHFATTQWTS MGFETAKEMKRRHIAKPFSMEKLLYQIAQAEAKKENGPTLSTISALLDELRDTELRQRRQLFEAGLHSSARYGSHDGNST VADGKKKPRKWLQLETSERRCQICQHLCYLSMVVQENENVVFCLECALRHVEKQKSCRGLKLMYRYDEEQIISLVNQICG KVSGKHGGIENCLNKPTPKRGPRKRATVDVPPSRLPSS A0A6I9KXB3 Zinc finger protein AEBP2 Homo sapiens 0.054535495999999996 2 Trichoplusia ni LEVO MAAAITDMADLEELSRLSPLPPGSPGSAARGRAEPPEEEEEEEEEEEEAEAEAVAALLLNGGSGGGGGGGGGGVGGGEAE TMSEPSPESASQAGEDEDEEEDDEEEEDESSSSGGGEEESSAESLVGSSGGSSSDETRSLSPGAASSSSGDGDGKEGLEE PKGPRGSQGGGGGGSSSSSVVSSGGDEGYGTGGGGSSATSGGRRGSLEMSSDGEPLSRMDSEDSISSTIMDVDSTISSGR STPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHML THSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDA QTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKL PKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSKQ Q6ZN18 G4 RNA Homo sapiens 0.007955823 1 GGGUAAGGGUAAGGGUAAGGGUAA ZINC ION 6.5409e-05 14 ZN singleParticle particle 7.9 25.0 C8H18N2O4S HEPES 50.0 KCl Potassium chloride 2.5 C3H8O3 Glycerol 0.01 np-40 substitute 1.0 C9H15O6P TCEP
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).
 Quantifoil R2/1 GOLD 300 CARBON CONTINUOUS 1.5 ETHANE 90 281 LEICA PLUNGER
3s of single side blotting.
We used streptavidin-affinity grid preparation method with biotin-labeled RNA at 100 nM concentration. PRC2 was applied in excess at 600 nM.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 0.6 2.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 1 18632 60.0
60 frames per movie
 1 3885383
Negative staining model
 3.4 FSC 0.143 CUT-OFF RELION 4.0-beta-2 217196 MAXIMUM LIKELIHOOD RELION 4.0-beta-2 MAXIMUM LIKELIHOOD RELION 4.0-beta-2 2 RELION 4.0-beta-2 emd_29578.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.03198 319.03198 319.03198 90.0 90.0 90.0 X Y Z -0.01349198 0.05151586 0.00025862228 0.0024155364 1.06344 1.06344 1.06344 0.014 AUTHOR consensus map of G4 RNA-mediated PRC2 dimer emd_29578_msk_1.map emd_29578_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.03198 319.03198 319.03198 90.0 90.0 90.0 X Y Z -0.024443109 0.076894894 0.0003768046 0.0024187032 1.06344 1.06344 1.06344 AUTHOR consensus map of G4 RNA-mediated PRC2 dimer after postprocessing with B-factor of -40 emd_29578_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.03198 319.03198 319.03198 90.0 90.0 90.0 X Y Z -0.017813947 0.057947163 0.00025826367 0.0028283135 1.06344 1.06344 1.06344 AUTHOR half map 1 of consensus map emd_29578_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.03198 319.03198 319.03198 90.0 90.0 90.0 X Y Z -0.018931836 0.057462305 0.00025901722 0.0028059604 1.06344 1.06344 1.06344 AUTHOR half map 2 of consensus map