eF-site ID 1y77-ABCDEFGHIJKLNPT PDB Code 1y77 Chain A, B, C, D, E, F, G, H, I, J, K, L, N, P, T Title Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP Classification TRANSCRIPTION,TRANSFERASE/DNA-RNA HYBRID Compound 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3' Source ORGANISM_COMMON: baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae; Sequence A:  VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETM DETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHF GHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQL VSRGGCGNTQPTIRKDGLKLVGSWKDEPELRVLSTEEILN IFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPS ISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAI EEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARL KGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKS IAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDS GDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPS LHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNL HVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLC GIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPK PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNI QKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKK VLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKA GRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQS VEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIM VHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGS DAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLL DEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQ TFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQN AQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNI EAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVP RLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIE HTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQS PWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWS EDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENI ERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTV PGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASD GSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMR CSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTG AFDVMIDEESLVKYMP B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL QDIICEDSTLIISFGKIYVTKPMVNESDGVTHALYPQEAR LRNLTYSSGLFVDVKKKVFIGRLPIMLRSKNCYLSEATES DLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFK KAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVND WQMLEMLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDIL QKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQD DRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTV ELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLN RYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCP AETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGME PLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLR RKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDE SLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYI DAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFT HCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG VFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPA GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSY MDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI APGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQV LVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGI TYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLS KVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVM YNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLM EASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIY QIHIPYAAKLLFQELMAMNITPRLYTDRSRDF C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ VVVRGIDTLQKKVASILLALTQMDQD D:  STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGE EEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELE SIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVI QLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISD DELERILKELSNLETLY 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 YDPKDALKNACNSIINKLGALKTNFETEWNLQTL L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL VQFEAR N:  AAGTACT P:  AAGACCAGGC T:  AGTACTTACGCCTGGTCTG Description Functional site 1) chain A residue 108 type sequence M description BINDING SITE FOR RESIDUE ZN A 1734 source : AC1 2) chain A residue 110 type sequence C description BINDING SITE FOR RESIDUE ZN A 1734 source : AC1 3) chain A residue 148 type sequence C description BINDING SITE FOR RESIDUE ZN A 1734 source : AC1 4) chain A residue 167 type sequence C description BINDING SITE FOR RESIDUE ZN A 1734 source : AC1 5) chain A residue 67 type sequence C description BINDING SITE FOR RESIDUE ZN A 1735 source : AC2 6) chain A residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN A 1735 source : AC2 7) chain A residue 77 type sequence C description BINDING SITE FOR RESIDUE ZN A 1735 source : AC2 8) chain A residue 80 type sequence H description BINDING SITE FOR RESIDUE ZN A 1735 source : AC2 9) chain B residue 1163 type sequence C description BINDING SITE FOR RESIDUE ZN B 1307 source : AC3 10) chain B residue 1166 type sequence C description BINDING SITE FOR RESIDUE ZN B 1307 source : AC3 11) chain B residue 1182 type sequence C description BINDING SITE FOR RESIDUE ZN B 1307 source : AC3 12) chain B residue 1185 type sequence C description BINDING SITE FOR RESIDUE ZN B 1307 source : AC3 13) chain C residue 86 type sequence C description BINDING SITE FOR RESIDUE ZN C 319 source : AC4 14) chain C residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN C 319 source : AC4 15) chain C residue 91 type sequence H description BINDING SITE FOR RESIDUE ZN C 319 source : AC4 16) chain C residue 92 type sequence C description BINDING SITE FOR RESIDUE ZN C 319 source : AC4 17) chain C residue 95 type sequence C description BINDING SITE FOR RESIDUE ZN C 319 source : AC4 18) chain I residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN I 203 source : AC5 19) chain I residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN I 203 source : AC5 20) chain I residue 29 type sequence C description BINDING SITE FOR RESIDUE ZN I 203 source : AC5 21) chain I residue 32 type sequence C description BINDING SITE FOR RESIDUE ZN I 203 source : AC5 22) chain I residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN I 204 source : AC6 23) chain I residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN I 204 source : AC6 24) chain I residue 103 type sequence C description BINDING SITE FOR RESIDUE ZN I 204 source : AC6 25) chain I residue 106 type sequence C description BINDING SITE FOR RESIDUE ZN I 204 source : AC6 26) chain I residue 108 type sequence H description BINDING SITE FOR RESIDUE ZN I 204 source : AC6 27) chain J residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN J 101 source : AC7 28) chain J residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN J 101 source : AC7 29) chain J residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN J 101 source : AC7 30) chain J residue 46 type sequence C description BINDING SITE FOR RESIDUE ZN J 101 source : AC7 31) chain L residue 31 type sequence C description BINDING SITE FOR RESIDUE ZN L 105 source : AC8 32) chain L residue 34 type sequence C description BINDING SITE FOR RESIDUE ZN L 105 source : AC8 33) chain L residue 48 type sequence C description BINDING SITE FOR RESIDUE ZN L 105 source : AC8 34) chain L residue 51 type sequence C description BINDING SITE FOR RESIDUE ZN L 105 source : AC8 35) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MG A 1736 source : AC9 36) chain A residue 483 type sequence D description BINDING SITE FOR RESIDUE MG A 1736 source : AC9 37) chain A residue 485 type sequence D description BINDING SITE FOR RESIDUE MG A 1736 source : AC9 38) chain P residue 10 type sequence C description BINDING SITE FOR RESIDUE MG A 1736 source : AC9 39) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 40) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 41) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 42) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 43) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 44) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 45) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 46) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 47) 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 48) 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 49) 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 50) 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 51) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 52) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 53) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 54) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 55) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 56) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 57) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 58) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 59) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 60) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 61) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 62) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5 63) 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 64) 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 65) 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 66) 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 67) 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 68) 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 69) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 70) 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 71) 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 72) 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 73) 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 74) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166

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