eF-site ID 5ipl-12ABCDEF PDB Code 5ipl Chain 1, 2, A, B, C, D, E, F click to enlarge Title SigmaS-transcription initiation complex with 4-nt nascent RNA Classification TRANSCRIPTION, TRANSFERASE/DNA/RNA Compound DNA-directed RNA polymerase subunit alpha Source Escherichia coli (strain K12) (5IPL) Sequence 1:  CACGTATGCTATAATGTGTGCAGTCTGACGCGG 2:  CCGCGTCAGACTCGTAGGATTATAGCATACGTG A:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK PQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDE RPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM ETNGTIDPEEAIRRAATILAEQLEAFVDLR B:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK PQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDE RPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM ETNGTIDPEEAIRRAATILAEQLEAFVD C:  YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEV YMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKG KTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELV PERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDV KLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLL AKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSA LVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEV DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLG DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLS EITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIE TPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGES SLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG ANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG VVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQN TCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD TKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDI LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPN GVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSE ELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDL APGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPI EDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAK GIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLS TFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK MHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG AAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPES FNVLLKEIRSLGINIELEDE D:  EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERD GLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRD IERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGD EFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVP LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRN EKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK QGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL ELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVC AAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA NGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAE RLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTV GRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEII SEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVS KAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSA AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFI STHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTA DILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGV CAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRT FHIGGAASKDITGGLPRVADLFEARRPKEPAILAEISGIV SFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGER VERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRL QGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYS RVKIANRELEANGKVGATYSRDLLGITKASLATESFISAA SFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY AYHQDRMRRRAAG E:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL F:  RVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRR RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVE KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQD DDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVG REIGLTRERVRQIQVEGLRRLREILQTQGLNIEALFL Description Functional site 1) chain C residue 1106 type sequence R description binding site for residue DPO C 1401 source : AC1 2) chain D residue 460 type sequence D description binding site for residue DPO C 1401 source : AC1 3) chain D residue 731 type sequence R description binding site for residue DPO C 1401 source : AC1 4) chain D residue 936 type sequence H description binding site for residue DPO C 1401 source : AC1 5) chain D residue 70 type sequence C description binding site for residue ZN D 1501 source : AC2 6) chain D residue 72 type sequence C description binding site for residue ZN D 1501 source : AC2 7) chain D residue 85 type sequence C description binding site for residue ZN D 1501 source : AC2 8) chain D residue 88 type sequence C description binding site for residue ZN D 1501 source : AC2 9) chain D residue 814 type sequence C description binding site for residue ZN D 1502 source : AC3 10) chain D residue 888 type sequence C description binding site for residue ZN D 1502 source : AC3 11) chain D residue 895 type sequence C description binding site for residue ZN D 1502 source : AC3 12) chain D residue 898 type sequence C description binding site for residue ZN D 1502 source : AC3 13) chain D residue 460 type sequence D description binding site for residue MG D 1503 source : AC4 14) chain D residue 462 type sequence D description binding site for residue MG D 1503 source : AC4 15) chain D residue 464 type sequence D description binding site for residue MG D 1503 source : AC4 16) chain C residue 813 type sequence E description binding site for residue MG D 1504 source : AC5 17) chain D residue 460 type sequence D description binding site for residue MG D 1504 source : AC5 18) chain F residue 288-307 type DNA_BIND sequence LEDVGREIGLTRERVRQIQV description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 19) chain D residue 895 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 20) chain D residue 898 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 21) chain D residue 72 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 22) chain D residue 85 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 23) chain D residue 88 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 24) chain D residue 460 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 25) chain D residue 462 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 26) chain D residue 464 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 27) chain D residue 814 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 28) chain D residue 888 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959 source Swiss-Prot : SWS_FT_FI1 29) chain C residue 1063-1075 type prosite sequence GDKMAGRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV source prosite : PS01166 30) chain F residue 118-131 type prosite sequence DLIEEGNLGLIRAV description SIGMA70_1 Sigma-70 factors family signature 1. DLIEeGnLGLIrAV source prosite : PS00715 31) chain F residue 287-313 type prosite sequence TLEDVGREIGLTRERVRQIQVEGLRRL description SIGMA70_2 Sigma-70 factors family signature 2. TleDVGreigLTrerVrQIQvegLrrL source prosite : PS00716

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