eF-site ID 4a3g-ABCDEFGHIJKL PDB Code 4a3g Chain A, B, C, D, E, F, G, H, I, J, K, L Title RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid Classification TRANSCRIPTION Compound DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 Source ORGANISM_COMMON: BAKER'S YEAST; ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; Sequence A:  GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMD ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM RQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLV SRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVL STEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVP PPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHN GAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPV KSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELD QVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA KYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPV LFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADF DGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPT PAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKD NGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVC AKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITET IAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFL NEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMS ACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVEN SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV KALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQS LDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGD LKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRR IIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRG KNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAF DWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTKK VTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKL IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLH FSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKND LFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITL RGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNL SEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVY NVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSN TGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQM APIGTGAFDVMIDEESLVKYMP B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL QDIICEDSTLIISFGKIYVTKPMVNESDGVTHALYPQEAR LRNLTYSSGLFVDVKKKVFIGRLPIMLRSKNCYLSEATES DLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFK KAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVND WQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEK RIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLL CALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKD IFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSS RAGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGL VCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEW GMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLR TLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVE DDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLV EYIDAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHAT TFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQ AMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRE LPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFF RSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDD GLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIV DQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT IGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIEC LLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGF EVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARG PMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKE RLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKI DIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ VVVRGIDTLQKKVASILLALTQMDQD D:  VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQG EEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKEL ESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAV IQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS DDELERILKELSNLETLY E:  DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLED FKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE FCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEK RELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRK SETSGRYASYRICM F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL IVDL G:  MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTG KFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI H:  SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD INVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDY DYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLN NLKQENAYLLIRR I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG LKRYCCRRMILTHVDLIEKFLRYNP K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTLA L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL VQFEAR Description (1)  DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2, RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 Functional site 1) chain A residue 107 type sequence C description BINDING SITE FOR RESIDUE ZN A 2456 source : AC1 2) chain A residue 110 type sequence C description BINDING SITE FOR RESIDUE ZN A 2456 source : AC1 3) chain A residue 148 type sequence C description BINDING SITE FOR RESIDUE ZN A 2456 source : AC1 4) chain A residue 167 type sequence C description BINDING SITE FOR RESIDUE ZN A 2456 source : AC1 5) chain A residue 67 type sequence C description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 6) chain A residue 69 type sequence T description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 7) chain A residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 8) chain A residue 77 type sequence C description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 9) chain A residue 80 type sequence H description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 10) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 11) chain A residue 483 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 12) chain A residue 485 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 13) chain B residue 1163 type sequence C description BINDING SITE FOR RESIDUE ZN B 2225 source : AC4 14) chain B residue 1166 type sequence C description BINDING SITE FOR RESIDUE ZN B 2225 source : AC4 15) chain B residue 1182 type sequence C description BINDING SITE FOR RESIDUE ZN B 2225 source : AC4 16) chain B residue 1185 type sequence C description BINDING SITE FOR RESIDUE ZN B 2225 source : AC4 17) chain C residue 86 type sequence C description BINDING SITE FOR RESIDUE ZN C 1269 source : AC5 18) chain C residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN C 1269 source : AC5 19) chain C residue 92 type sequence C description BINDING SITE FOR RESIDUE ZN C 1269 source : AC5 20) chain C residue 95 type sequence C description BINDING SITE FOR RESIDUE ZN C 1269 source : AC5 21) chain I residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN I 1121 source : AC6 22) chain I residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN I 1121 source : AC6 23) chain I residue 29 type sequence C description BINDING SITE FOR RESIDUE ZN I 1121 source : AC6 24) chain I residue 32 type sequence C description BINDING SITE FOR RESIDUE ZN I 1121 source : AC6 25) chain I residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN I 1122 source : AC7 26) chain I residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN I 1122 source : AC7 27) chain I residue 103 type sequence C description BINDING SITE FOR RESIDUE ZN I 1122 source : AC7 28) chain I residue 106 type sequence C description BINDING SITE FOR RESIDUE ZN I 1122 source : AC7 29) chain J residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN J 1066 source : AC8 30) chain J residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN J 1066 source : AC8 31) chain J residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN J 1066 source : AC8 32) chain J residue 46 type sequence C description BINDING SITE FOR RESIDUE ZN J 1066 source : AC8 33) chain L residue 31 type sequence C description BINDING SITE FOR RESIDUE ZN L 1071 source : AC9 34) chain L residue 34 type sequence C description BINDING SITE FOR RESIDUE ZN L 1071 source : AC9 35) chain L residue 48 type sequence C description BINDING SITE FOR RESIDUE ZN L 1071 source : AC9 36) chain L residue 51 type sequence C description BINDING SITE FOR RESIDUE ZN L 1071 source : AC9 37) chain F residue 86-100 type prosite sequence TKYERARILGTRALQ description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ source prosite : PS01111 38) chain I residue 7 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 39) chain I residue 10 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 40) chain I residue 29 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 41) chain I residue 32 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 42) chain I residue 75 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 43) chain I residue 78 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 44) chain I residue 103 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 45) chain I residue 106 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 46) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5 47) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 48) chain E residue 147-160 type prosite sequence HELVPKHIRLSSDE description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE source prosite : PS01110 49) chain J residue 2-11 type prosite sequence IVPVRCFSCG description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG source prosite : PS01112 50) chain K residue 35-66 type prosite sequence FEKEDHTLGNLIRAELLNDRKVLFAAYKVEHP description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP source prosite : PS01154 51) chain C residue 31-71 type prosite sequence NSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLI P description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP source prosite : PS00446 52) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 53) chain I residue 6-32 type prosite sequence FCRDCNNMLYPREDKENNRLLFECRTC description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCrDCNNMLypredkennrllfeCrtC source prosite : PS01030 54) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 55) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 56) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 57) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 58) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 59) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 60) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 61) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 62) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 63) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 64) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 65) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 66) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 67) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 68) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 69) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 70) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 71) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 72) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2

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