eF-site ID 5c44-ABCDEFGHIJKL PDB Code 5c44 Chain A, B, C, D, E, F, G, H, I, J, K, L Title Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Classification TRANSFERASE/DNA/RNA Compound DNA-directed RNA polymerase II subunit RPB1 Source ORGANISM_COMMON: Baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae (strain ATCC 204508 / S288c); Sequence A:  VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETM DETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHF GHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQL VSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRV LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPV PPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEH NGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRP VKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDP VLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCM GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQV CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITE TIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQM SACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ SLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILG DLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL FHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPG HAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVI PEDEEIIQLHFSFDQQSPWLLRLELDRAAMNDKDLTMGQV GERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPAEEDHML KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVK EPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLG IEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDD CRGVSENVILGQMAPIGTGAFDVMIDEESLVKYM B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL QDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTK PMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEA IDVPGRELKYELIDSESGKVFIGRLPIMLRSKNCYLSEAT ESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQV FKKAAPSPISHVAEIRSALEKGRFISTLQVKLYGRSSART IATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQ MLEMLKPCVEDGFVIQDRETALDFIGRLGIRIQYAKDILQ KEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDD RDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVE EAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRA GVSQVLNRYTYSSTLSHLRRTNTPIGRDGKPRQLHNTHWG LVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETL RTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV EDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGL VEYIDAEEEESILIAMQPEDLEPAEAKRIRATTFTHCEIH PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN YNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAI VAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVR VSGEDVIIGKTTPISPDEEELGTAYHSKRDASTPLRSTEN GIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQ KGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHL IECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQS RGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHAR ARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASF LKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCD NKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF C:  EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPT LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYS RDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSN LMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGI AKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQ SKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQV VVRGIDTLQKKVASILLALTQMDQD D:  STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGE EEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKEL ESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAV IQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS DDELERILKELSNLETLY E:  DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLED FKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE FCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEK RELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRK SETSGRYASYRICM F:  LKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVF VDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSV EELIVDL G:  MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTG KFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI H:  MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTL DINVELFPVAAQDSLTVTIASSLNATRSWRPPQAGDRSLA DDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYR NLNNLQENAYLLIRR I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG LKRYCCRRMILTHVDLIEKFLRYNP K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTLA L:  LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQ FEAR Description (1)  DNA-directed RNA polymerase II /RNA/DNA Complex Functional site 1) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 2) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 3) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 4) chain A residue 1085 type catalytic sequence H description 788 source MCSA : MCSA1 5) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5 6) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 7) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 8) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 9) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 10) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 11) 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 12) 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 13) 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 14) 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 15) 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 16) 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 17) 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 18) 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 19) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 20) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 21) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 22) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 23) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 24) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 25) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 26) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 27) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 28) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 29) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 30) 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 31) 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 32) 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 33) 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 34) 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 35) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 36) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 37) 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

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