eF-site ID 4a3l-ABCDEFGHIJKLNPT PDB Code 4a3l Chain A, B, C, D, E, F, G, H, I, J, K, L, N, P, T Title RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP 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 DWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLN TKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQ AKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEII QLHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTF KNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLEN ITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDG VNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYK EVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFN RSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL GQMAPIGTGAFDVMIDEESLVKYMP 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 N:  AAGTACTTG P:  ACCAGGA T:  CAAGTACTTTTTCCXGGT 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 RPABC1, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 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 70 type sequence C description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 7) chain A residue 77 type sequence C description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 8) chain A residue 80 type sequence H description BINDING SITE FOR RESIDUE ZN A 2457 source : AC2 9) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 10) chain A residue 483 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 11) chain A residue 485 type sequence D description BINDING SITE FOR RESIDUE MG A 2458 source : AC3 12) chain P residue 10 type sequence A 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 A residue 446 type sequence R description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 38) chain A residue 448 type sequence P description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 39) chain A residue 479 type sequence N description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 40) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 41) chain A residue 1082 type sequence N description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 42) chain B residue 769 type sequence Y description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 43) chain B residue 987 type sequence K description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 44) chain B residue 1020 type sequence R description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 45) chain P residue 10 type sequence A description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 46) chain T residue 18 type sequence T description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 47) chain T residue 19 type sequence T description BINDING SITE FOR RESIDUE APC P 1011 source : BC1 48) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 49) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 50) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 51) 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 52) 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 53) 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 54) 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 55) 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 56) 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 57) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 58) 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 59) 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 60) 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 61) 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 62) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 63) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 64) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 65) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 66) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 67) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 68) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 69) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 70) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 71) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 72) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 73) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 74) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 75) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 76) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 77) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 78) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 79) 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 80) 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 81) 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 82) 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 83) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5

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