RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei

2025-06-11 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBj PDBj 2024-01-09 2025-05-07 2025-05-07 2025-06-11 Japan Society for the Promotion of Science (JSPS) JP20H03201 Japan Japan Society for the Promotion of Science (JSPS) JP20H05690 Japan Japan Society for the Promotion of Science (JSPS) JP22K15033 Japan Japan Society for the Promotion of Science (JSPS) JP23K17392 Japan Japan Society for the Promotion of Science (JSPS) JP22KJ0858 Japan Japan Society for the Promotion of Science (JSPS) JP22K06098 Japan Japan Society for the Promotion of Science (JSPS) JP20H00449 Japan Japan Society for the Promotion of Science (JSPS) JP23H05475 Japan Japan Science and Technology JPMJER1901 Japan Japan Agency for Medical Research and Development (AMED) JP22ama121009 Japan RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Kujirai T Kato J Yamamoto K Hirai S Negishi L Ogasawara M Takizawa Y Kurumizaka H complex, nucleus, TRANSCRIPTION-DNA-RNA COMPLEX Kujirai T Kato J Yamamoto K Hirai S Fujii T Maehara K Harada A Negishi L Ogasawara M Yamaguchi Y Ohkawa Y Takizawa Y Kurumizaka H Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis. Nat Commun UK 16 4724 4724 2025 40436841 doi:10.1038/s41467-025-59580-x 2041-1723 8xso FULLOVERLAP RNA polymerase II complexes isolated from HeLa cell nuclei RNA polymerase II complexes isolated from HeLa cell nuclei 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Homo sapiens DNA-directed RNA polymerase II subunit RPB1 Homo sapiens 0.21742004699999998 1 LEVO MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTE CPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEM DNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDN ELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNID RLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV MNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGIL CKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPF GFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR NSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLL FNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLG VPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMD DDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSN DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPW NQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAY EPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSP SYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPASPKYT PTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN P24928 2.7.7.6 DNA-directed RNA polymerase II subunit RPB2 Homo sapiens 0.134071453 1 LEVO MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEE PPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTY CLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNF IGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLL AFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAA IADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHI DQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA VDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL ESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV P30876 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Homo sapiens 0.033630387 1 Homo sapiens LEVO MHHHHHHDYKDDDDKGHMPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEF IAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYV EQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPN GKPERFYYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN P19387 DNA-directed RNA polymerase II subunit RPB4 Homo sapiens 0.016331255 1 LEVO MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETI ASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY O15514 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Homo sapiens 0.024584223000000002 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ P19388 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Homo sapiens 0.014491025999999999 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD P61218 DNA-directed RNA polymerase II subunit RPB7 Homo sapiens 0.019314282999999998 1 LEVO MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLVS P62487 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Homo sapiens 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF P52434 DNA-directed RNA polymerase II subunit RPB9 Homo sapiens 0.014541220999999998 1 LEVO MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPR TEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE P36954 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Homo sapiens 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK P62875 DNA-directed RNA polymerase II subunit RPB11-a Homo sapiens 0.013310283999999999 1 LEVO MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE P52435 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Homo sapiens 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR P53803 DNA Homo sapiens 0.011395343999999998

The DNA sequence in this structure is unknown because it is an average of genomic DNA regions bound to the RNA polymerase II.

1 (DT)(DA)(DG)(DT)(DA)(DA)(DA)(DG)(DA)(DC)(DC)(DA)(DG)(DG)(DC)(DT)(DT)(DA)(DA)(DG) (DT)(DA)(DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DT)(DC)(DT)(DG)(DT)(DC) DNA RNA Homo sapiens 0.003529194

The RNA sequence in this structure is unknown because it is an average of RNA bound to the RNA polymerase II on genomic DNA.

1 AAGACCAGGCU DNA Homo sapiens 0.011373346999999999

The DNA sequence in this structure is unknown because it is an average of genomic DNA regions bound to the RNA polymerase II.

1 (DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DA)(DA)(DG)(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DC)(DT)(DA) DNA ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 5FLM 2.7 FSC 0.143 CUT-OFF 523284 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_38624.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.020531252 0.06154948 0.00015544044 0.0014904585 1.06 1.06 1.06 0.0077 AUTHOR ::::EMDATABANK.org::::EMD-38624:::: emd_38624_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.019068131 0.060055535 0.000008377336 0.0020686162 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-38624:::: emd_38624_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.021373082 0.06178575 0.000007467788 0.002084028 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-38624::::