eF-site ID 4x67-ABCEFHIJKLRT PDB Code 4x67 Chain A, B, C, E, F, H, I, J, K, L, R, T Title Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions. Classification TRANSCRIPTION/DNA Compound DNA-directed RNA polymerase II subunit RPB1 Source ORGANISM_COMMON: Baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae (strain ATCC 204508 / S288c); Sequence A:  GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMD ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM RQALAIKDSKKRFAAIWTLCKTKMVCETDVPSLVSRGGCG NTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFT SLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGED DLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNL MGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVV TPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRV KVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAE LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSV AIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKK TVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQAN LLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDL NNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGG REGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSL GNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDR KFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSD LTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHP GEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVAKN MKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIAS EIYYDPDPRSTVIPEDEEIIQLHFSQQSPWLLRLELDRAA MNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCR VVAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKV PSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNS FIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALL VDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFE AGASAELDDCRGVSENVILGQMAPIGTGAFDVMI B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL QDIICEDSTLIISFGKIYVTKPMVNESDGVTHALYPQEAR LRNLTYSSGLFVDVKKKVFIGRLPIMLRSKNCYLSEATES DLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFK KAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVND WQMLEMLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDIL QKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQD DRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTV ELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLN RYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEG QACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYV PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDIN PEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKE LKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEE SILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHP SMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNY NVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIV AIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKK YGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRV SGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQ DGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRRED MPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS GNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTG KKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQP VEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAF RVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPY AAKLLFQELMAMNITPRLYTDRSRDF C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ VVVRGIDTLQKKVASILLALTQMDQD E:  DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLED FKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE FCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEK RELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRK SETSGRYASYRICM F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL IVDL H:  SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD INVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDY DYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLN NLKQENAYLLIRR I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG LKRYCCRRMILTHVDLIEKFLRYNP K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTL L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL VQFEAR R:  AUCGAGAUA T:  AXTCTCGATG Description (1)  DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerases I, II, and III subunit RPABC1, iaDNA-directed RNA polymerases I, II, and III subunit RPABC2, 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/RNA Complex Functional site 1) chain A residue 107 type sequence C description binding site for residue ZN A 1801 source : AC1 2) chain A residue 108 type sequence M description binding site for residue ZN A 1801 source : AC1 3) chain A residue 110 type sequence C description binding site for residue ZN A 1801 source : AC1 4) chain A residue 148 type sequence C description binding site for residue ZN A 1801 source : AC1 5) chain A residue 166 type sequence G description binding site for residue ZN A 1801 source : AC1 6) chain A residue 167 type sequence C description binding site for residue ZN A 1801 source : AC1 7) chain A residue 67 type sequence C description binding site for residue ZN A 1802 source : AC2 8) chain A residue 68 type sequence Q description binding site for residue ZN A 1802 source : AC2 9) chain A residue 70 type sequence C description binding site for residue ZN A 1802 source : AC2 10) chain A residue 77 type sequence C description binding site for residue ZN A 1802 source : AC2 11) chain A residue 80 type sequence H description binding site for residue ZN A 1802 source : AC2 12) chain B residue 1163 type sequence C description binding site for residue ZN B 1301 source : AC3 13) chain B residue 1166 type sequence C description binding site for residue ZN B 1301 source : AC3 14) chain B residue 1182 type sequence C description binding site for residue ZN B 1301 source : AC3 15) chain B residue 1185 type sequence C description binding site for residue ZN B 1301 source : AC3 16) chain C residue 86 type sequence C description binding site for residue ZN C 401 source : AC4 17) chain C residue 88 type sequence C description binding site for residue ZN C 401 source : AC4 18) chain C residue 92 type sequence C description binding site for residue ZN C 401 source : AC4 19) chain C residue 95 type sequence C description binding site for residue ZN C 401 source : AC4 20) chain I residue 7 type sequence C description binding site for residue ZN I 201 source : AC5 21) chain I residue 10 type sequence C description binding site for residue ZN I 201 source : AC5 22) chain I residue 29 type sequence C description binding site for residue ZN I 201 source : AC5 23) chain I residue 32 type sequence C description binding site for residue ZN I 201 source : AC5 24) chain I residue 75 type sequence C description binding site for residue ZN I 202 source : AC6 25) chain I residue 78 type sequence C description binding site for residue ZN I 202 source : AC6 26) chain I residue 103 type sequence C description binding site for residue ZN I 202 source : AC6 27) chain I residue 106 type sequence C description binding site for residue ZN I 202 source : AC6 28) chain J residue 7 type sequence C description binding site for residue ZN J 101 source : AC7 29) chain J residue 10 type sequence C description binding site for residue ZN J 101 source : AC7 30) chain J residue 45 type sequence C description binding site for residue ZN J 101 source : AC7 31) chain J residue 46 type sequence C description binding site for residue ZN J 101 source : AC7 32) chain L residue 31 type sequence C description binding site for residue ZN L 101 source : AC8 33) chain L residue 34 type sequence C description binding site for residue ZN L 101 source : AC8 34) chain L residue 48 type sequence C description binding site for residue ZN L 101 source : AC8 35) chain L residue 51 type sequence C description binding site for residue ZN L 101 source : AC8 36) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 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 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 E residue 147-160 type prosite sequence HELVPKHIRLSSDE description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE source prosite : PS01110 48) 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 49) 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 50) 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 51) 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 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 B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 54) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 55) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 56) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 57) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 58) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 59) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 60) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 61) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 62) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 63) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 64) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 65) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 66) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 67) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 68) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 69) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 70) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 71) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2

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