De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS

2024-01-03 REL PDBj PDBj PDBj 2023-09-08 2023-12-06 2023-12-06 2024-01-03 Not funded De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS Chen X Liu W Wang Q Wang X Ren Y Qu X Li W Xu Y transcribing complex, de novo transcription initiation, early elongation complex (EEC), TRANSCRIPTION Chen X Liu W Wang Q Wang X Ren Y Qu X Li W Xu Y Structural visualization of transcription initiation in action. Science US 382 eadi5120 eadi5120 2023 38127763 doi:10.1126/science.adi5120 1095-9203 0038 SCIEAS EMD-31111 other EM volume

TFIID-based holo PIC on SCP promoter

EMD-37413 other EM volume

De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS.

EMD-37412 other EM volume

De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS

EMD-37411 other EM volume

De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS.

EMD-37410 other EM volume

De novo transcribing complex 16 (TC16), the early elongation complex with Pol II positioned 16nt downstream of TSS.

EMD-37409 other EM volume

De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS.

EMD-37408 other EM volume

De novo transcribing complex 14 (TC14), the early elongation complex with Pol II positioned 14nt downstream of TSS.

EMD-37407 other EM volume

De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS.

EMD-37405 other EM volume

De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS.

EMD-37404 other EM volume

De novo transcribing complex 10 (TC10), the early elongation complex with Pol II positioned 10nt downstream of TSS.

EMD-37403 other EM volume

Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS.

EMD-37402 other EM volume

Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS.

EMD-37401 other EM volume

Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS.

EMD-37400 other EM volume

Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS.

EMD-37399 other EM volume

Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS.

EMD-37398 other EM volume

Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS.

EMD-37396 other EM volume

Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS.

EMD-37395 other EM volume

Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS.

8wav FULLOVERLAP Structure of transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS Structure of transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 RNA POLYMERASE II 1 7 8 9 10 11 12 13 14 15 16 17 18 Sus scrofa TFIIF 1 2 3 Homo sapiens DNA 1 4 5 synthetic construct RNA 1 6 synthetic construct Alpha-amanitin 1 1 Amanita phalloides Alpha-amanitin Amanita phalloides 0.000939004 1 LEVO (ILX)(TRX)GIG(CSX)N(HYP) P85421 General transcription factor IIF subunit 1 Homo sapiens 0.058343578 1 Homo sapiens LEVO MAALGPSSQNVTEYVVRVPKNTTKKYNIMAFNAADKVNFATWNQARLERDLSNKKIYQEEEMPESGAGSEFNRKLREEAR RKKYGIVLKEFRPEDQPWLLRVNGKSGRKFKGIKKGGVTENTSYYIFTQCPDGAFEAFPVHNWYNFTPLARHRTLTAEEA EEEWERRNKVLNHFSIMQQRRLKDQDQDEDEEEKEKRGRRKASELRIHDLEDDLEMSSDASDASGEEGGRVPKAKKKAPL AKGGRKKKKKKGSDDEAFEDSDDGDFEGQEVDYMSDGSSSSQEEPESKAKAPQQEEGPKGVDEQSDSSEESEEEKPPEED KEEEEEKKAPTPQEKKRRKDSSEESDSSEESDIDSEASSALFMAKKKTPPKRERKPSGGSSRGNSRPGTPSAEGGSTSST LRAAASKLEQGKRVSEMPAAKRLRLDTGPQSLSGKSTPQPPSGKTTPNSGDVQVTEDAVRRYLTRKPMTTKDLLKKFQTK KTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE P35269 General transcription factor IIF subunit 2 Homo sapiens 0.028427309 1 Homo sapiens LEVO MAERGELDLTGAKQNTGVWLVKVPKYLSQQWAKASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGGKPASVSAPRE HPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQ YNIEYERKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYR HYQGEEKSD P13984 3.6.4.12 non-template DNA synthetic construct 0.030626565999999997 1 (DA)(DA)(DG)(DG)(DG)(DC)(DG)(DC)(DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG)(DG)(DG) (DG)(DT)(DG)(DG)(DT)(DT)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DT)(DT)(DC)(DT)(DT)(DC) (DA)(DT)(DC)(DA)(DA)(DC)(DT)(DT)(DC)(DA)(DT)(DG)(DG)(DA)(DC)(DT)(DT)(DC)(DG)(DA) (DG)(DC)(DC)(DG)(DA)(DG)(DC)(DA)(DG)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DA)(DC)(DG) (DG)(DA)(DC)(DC)(DA)(DT)(DG)(DT)(DC)(DC)(DG)(DA)(DA)(DA)(DC)(DT)(DG)(DA)(DC) DNA template DNA synthetic construct 0.030457455 1 (DG)(DT)(DC)(DA)(DG)(DT)(DT)(DT)(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DG)(DG)(DT)(DC)(DC) (DG)(DT)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG)(DC)(DT) (DC)(DG)(DA)(DA)(DG)(DT)(DC)(DC)(DA)(DT)(DG)(DA)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DG) (DA)(DA)(DG)(DA)(DA)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC)(DA)(DA)(DC)(DC)(DA)(DC)(DC) (DC)(DC)(DC)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DG)(DG)(DC)(DG)(DC)(DC)(DC)(DT)(DT) DNA RNA synthetic construct 0.003975319 1 (ATP)UCAACUUCAU(G2L) DNA-directed RNA polymerase subunit Sus scrofa 0.217450078 1 LEVO MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTE CPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEM DNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDN ELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNID RLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV MNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGIL CKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPF GFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR NSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLL FNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLG VPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMD DDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSN DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPW NQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAY EPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSP SYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYT PTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN A0A8D1DPV6 DNA-directed RNA polymerase subunit beta Sus scrofa 0.134041422 1 LEVO MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEE PPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTY CLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNF IGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLL AFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAA IADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHI DQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA VDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL EGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV A0A4X1TVZ5 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Sus scrofa 0.031439074 1 LEVO MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVD KLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELR LRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN I3LCH3 DNA-directed RNA polymerase II subunit RPB4 Sus scrofa 0.016331255 1 LEVO MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETI ASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY A0A481BYI6 DNA-directed RNA polymerase II subunit E Sus scrofa 0.024644318 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ A0A4X1VTX4 DNA-directed RNA polymerase II subunit F Sus scrofa 0.014477001 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD A0A4X1VEK9 DNA-directed RNA polymerase II subunit RPB7 Sus scrofa 0.019314282999999998 1 LEVO MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLVS A0A4X1VKG7 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Sus scrofa 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF I3LCB2 DNA-directed RNA polymerase II subunit RPB9 Sus scrofa 0.014541220999999998 1 LEVO MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPR TEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE P60899 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Sus scrofa 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK A0A493TD97 DNA-directed RNA polymerase II subunit RPB11-a Sus scrofa 0.013310283999999999 1 LEVO MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE F1RKE4 RPB12 Sus scrofa 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR A0A4X1TRS6 ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate 0.0005372069999999999 1 W0F singleParticle particle 7.9 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.5 GATAN K3 (6k x 4k) 50.0 1 5FLM 2.72 FSC 0.143 CUT-OFF 539000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_37406.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 426.88 426.88 426.88 90.0 90.0 90.0 X Y Z -5.1650577 7.703932 0.00426456 0.11477463 1.334 1.334 1.334 0.7 AUTHOR ::::EMDATABANK.org::::EMD-37406:::: emd_37406_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 426.88 426.88 426.88 90.0 90.0 90.0 X Y Z -0.052511092 0.2849629 0.0030421347 0.024164608 1.334 1.334 1.334 AUTHOR ::::EMDATABANK.org::::EMD-37406:::: Overall map of TC12 emd_37406_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 426.88 426.88 426.88 90.0 90.0 90.0 X Y Z -0.8293742 2.3642843 0.0035699832 0.06502448 1.334 1.334 1.334 AUTHOR ::::EMDATABANK.org::::EMD-37406:::: emd_37406_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 426.88 426.88 426.88 90.0 90.0 90.0 X Y Z -0.7593179 2.4709282 0.0035680954 0.06502276 1.334 1.334 1.334 AUTHOR ::::EMDATABANK.org::::EMD-37406::::