Cryo-EM structure of PRC2 in complex with the long isoform of AEBP2

2025-12-03 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2022-10-09 2024-07-31 2024-07-31 2025-12-03 Australian Research Council (ARC) DP190103407 Australia Other private Sylvia and Charles Viertel Senior Medical Research Fellowship Australia National Health and Medical Research Council (NHMRC, Australia) APP1162921 Australia National Health and Medical Research Council (NHMRC, Australia) APP1184637 Australia National Health and Medical Research Council (NHMRC, Australia) APP2011767 Australia Australian Research Council (ARC) DE180100219 Australia National Health and Medical Research Council (NHMRC, Australia) APP1196365 Australia Cryo-EM structure of PRC2 in complex with the long isoform of AEBP2 Boudes M Zhang Q Flanigan SF Davidovich C Polycomb repressive complex 2 Histone methyltransferase, GENE REGULATION Mucha M Lai Z McKenzie NJ Matra F Boudes M Flanigan SF Alejo-Vinogradova MT Monger C Zhang Q Nimmo D Healy E Silva AJ Angelov D Reck DM Holland G Atmaca ZE King HE Hamilton M Glancy E Nolan J Weatheritt RJ Bell O Vermeulen M Davidovich C Bracken AP Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2. Embo J. UK 2025 41168462 doi:10.1038/s44318-025-00616-9 1460-2075 0897 EMJODG 8eqv FULLOVERLAP EMDB EMD-28547 associated EM volume

Ternary complex of PRC2 with long isoform of AEBP2 Ternary complex of PRC2 with long isoform of AEBP2 0 1 2 3 4 5 Homo sapiens Histone-binding protein RBBP4 Homo sapiens 0.047709527 1 Trichoplusia ni LEVO MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLV IASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSK PDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEI FQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQ VWQMAENIYNDEDPEGSVDPEGQGS Q09028 Zinc finger protein AEBP2 Homo sapiens 0.054535495999999996 1 Trichoplusia ni LEVO MAAAITDMADLEELSRLSPLPPGSPGSAARGRAEPPEEEEEEEEEEEEAEAEAVAALLLNGGSGGGGGGGGGGVGGGEAE TMSEPSPESASQAGEDEDEEEDDEEEEDESSSSGGGEEESSAESLVGSSGGSSSDETRSLSPGAASSSSGDGDGKEGLEE PKGPRGSQGGGGGGSSSSSVVSSGGDEGYGTGGGGSSATSGGRRGSLEMSSDGEPLSRMDSEDSISSTIMDVDSTISSGR STPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHML THSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDA QTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKL PKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSKQ Q6ZN18 Polycomb protein EED Homo sapiens 0.050267690999999996 1 Trichoplusia ni LEVO MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTPNAPGRKSWGKGKWKSKKCKY SFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSH PLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLIL SKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAK CTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR O75530 Histone-lysine N-methyltransferase EZH2 Homo sapiens 0.08549229700000001 1 Trichoplusia ni LEVO MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWKQRRIQPVHILTSVSSLRGT RECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGD RECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRKNTETALDNKPC GPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEK KDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNRFPGC RCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISE YCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE ELFFDYRYSQADALKYVGIEREMEIP Q15910 2.1.1.356 Polycomb protein SUZ12 Homo sapiens 0.083181922 1 Trichoplusia ni LEVO MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQ ADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLT FTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQ EMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTI AVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVEQQRTYSSG HNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFV ENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK ALETDSVSGVSKQSKKQKL Q15022 singleParticle particle 2.4 7.5 200.0 NaCl sodium chloride 20.0 HEPES 1.0 TCEP 0.01 NP-40

200 mM NaCl, 20 mM HEPES pH 7.5, 1 mM TCEP, 0.01% NP-40

Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE 120 AIR

0.24 mBar, 120 s, 10 mAmp

ETHANE 100 277 FEI VITROBOT MARK IV

Blotting 3 seconds.

Prior to cryo-EM sample preparation, complexes were PEGylated at 0.9 mg/mL with 5 mM MS(PEG)4 Methyl-PEG-NHS-Ester (ThermoFisher Scientific) for 2 h at 4oC.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum ER 10 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 847067 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 5WAI

5WAI, 6WKR

1 C1 3.64 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 non-uniform refinement 45024 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 ab initio MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 non-uniform refinement 1 emd_28547.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 309.6 309.6 309.6 90.0 90.0 90.0 X Y Z -0.2949924 0.802014 0.0012688375 0.026894417 0.86 0.86 0.86 0.18 AUTHOR ::::EMDATABANK.org::::EMD-28547:::: emd_28547_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 309.6 309.6 309.6 90.0 90.0 90.0 X Y Z -1.1228635 1.9637727 0.0012688374 0.04342683 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-28547:::: emd_28547_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 309.6 309.6 309.6 90.0 90.0 90.0 X Y Z -0.48222026 1.0713892 0.0014407124 0.05729045 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-28547:::: emd_28547_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 309.6 309.6 309.6 90.0 90.0 90.0 X Y Z -0.5048149 1.0681953 0.0014712377 0.057194397 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-28547::::