eF-site ID 5flm-ABCDEFGHIJKL PDB Code 5flm Chain A, B, C, D, E, F, G, H, I, J, K, L Title Structure of transcribing mammalian RNA polymerase II Classification TRANSCRIPTION Compound DNA-DIRECTED RNA POLYMERASE Source ORGANISM_COMMON: BOVINE; ORGANISM_SCIENTIFIC: BOS TAURUS; Sequence A:  SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGG RPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIEL AKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDIL AKSKGQPKKRLTHVYDLCKGKNICEHGGCGRYQPRIRRSG LELYAEWKKILLSPERVHEIFKRISDEECFVLGMEPRYAR PEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIV KINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPG LPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSAR TVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQE LVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGY KVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRM IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLL MFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIR THSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKS LGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEG HTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNE LEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYN NFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKH RTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGR EGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSIN QVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDY TNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDRE VLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDL HPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIH LRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPG EMVGALAAQSLGEPATQMTLNTFHKNVTLGVPRLKELINI SKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVT ANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPW LLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDD NAEKLVLRIRIMNSDENKMDDDVFLRCIESNMLTDMTLQG IEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDG VSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALER ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVN RQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIML GQLAPAGTGCFDLLLDAEKCKYGMEIP B:  EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSV QRIVEDAPPIDLQPPRYLLKFEQIYLSKPTHWERDGAPSP MMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKT FIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFII NGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLEN SSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEV PIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDE AFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEM LPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDH YGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGK DFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVS QVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWG MVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE WSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTL RKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLI VEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDT LEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVC ASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTL AHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTG YNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEE VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVII GKTVTLPTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCK IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDAT PFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQ ELMSMSIAPRMMSV C:  PYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAE VPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDK LQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI SNSPRVIPVTSDDILIVKLRKGQELRLRAYAKKGFGKEHA KWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDED ESQAPYDPNGKPERFYYNVESCGSLRPETIVLSALSGLKK KLSDLQTQLSHEIQSDV D:  EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAED EQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLH KFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDD IQTKRSFQ E:  DDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFK AQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPK VGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDM APKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLA RYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAG RYITYRLVQ F:  QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEG ETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII TD G:  MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTG KYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLV H:  AGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLIL DVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDR PSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGL LMRLQGDANNLHGFEVDSRVYLLMKKLA I:  VGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNS CIYVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGH KEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE J:  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGL KRYCCRRMLLAHVDLIEKLLNYAPLEK K:  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDH TLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEG L:  MIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVV FDAR Description (1)  DNA-DIRECTED RNA POLYMERASE (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 71 type sequence C description BINDING SITE FOR RESIDUE ZN A 2488 source : AC1 2) chain A residue 73 type sequence T description BINDING SITE FOR RESIDUE ZN A 2488 source : AC1 3) chain A residue 74 type sequence C description BINDING SITE FOR RESIDUE ZN A 2488 source : AC1 4) chain A residue 81 type sequence C description BINDING SITE FOR RESIDUE ZN A 2488 source : AC1 5) chain A residue 84 type sequence H description BINDING SITE FOR RESIDUE ZN A 2488 source : AC1 6) chain A residue 111 type sequence C description BINDING SITE FOR RESIDUE ZN A 2489 source : AC2 7) chain A residue 114 type sequence C description BINDING SITE FOR RESIDUE ZN A 2489 source : AC2 8) chain A residue 154 type sequence C description BINDING SITE FOR RESIDUE ZN A 2489 source : AC2 9) chain A residue 183 type sequence G description BINDING SITE FOR RESIDUE ZN A 2489 source : AC2 10) chain A residue 184 type sequence C description BINDING SITE FOR RESIDUE ZN A 2489 source : AC2 11) chain A residue 495 type sequence D description BINDING SITE FOR RESIDUE MG A 2490 source : AC3 12) chain A residue 497 type sequence D description BINDING SITE FOR RESIDUE MG A 2490 source : AC3 13) chain A residue 499 type sequence D description BINDING SITE FOR RESIDUE MG A 2490 source : AC3 14) chain B residue 1119 type sequence C description BINDING SITE FOR RESIDUE ZN B 2175 source : AC4 15) chain B residue 1122 type sequence C description BINDING SITE FOR RESIDUE ZN B 2175 source : AC4 16) chain B residue 1137 type sequence C description BINDING SITE FOR RESIDUE ZN B 2175 source : AC4 17) chain B residue 1140 type sequence C description BINDING SITE FOR RESIDUE ZN B 2175 source : AC4 18) chain C residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN C 1272 source : AC5 19) chain C residue 90 type sequence C description BINDING SITE FOR RESIDUE ZN C 1272 source : AC5 20) chain C residue 94 type sequence C description BINDING SITE FOR RESIDUE ZN C 1272 source : AC5 21) chain C residue 97 type sequence C description BINDING SITE FOR RESIDUE ZN C 1272 source : AC5 22) chain I residue 17 type sequence C description BINDING SITE FOR RESIDUE ZN I 1126 source : AC6 23) chain I residue 20 type sequence C description BINDING SITE FOR RESIDUE ZN I 1126 source : AC6 24) chain I residue 39 type sequence C description BINDING SITE FOR RESIDUE ZN I 1126 source : AC6 25) chain I residue 42 type sequence C description BINDING SITE FOR RESIDUE ZN I 1126 source : AC6 26) chain I residue 86 type sequence C description BINDING SITE FOR RESIDUE ZN I 1127 source : AC7 27) chain I residue 89 type sequence C description BINDING SITE FOR RESIDUE ZN I 1127 source : AC7 28) chain I residue 114 type sequence C description BINDING SITE FOR RESIDUE ZN I 1127 source : AC7 29) chain I residue 119 type sequence C description BINDING SITE FOR RESIDUE ZN I 1127 source : AC7 30) chain J residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN J 1068 source : AC8 31) chain J residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN J 1068 source : AC8 32) chain J residue 44 type sequence C description BINDING SITE FOR RESIDUE ZN J 1068 source : AC8 33) chain J residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN J 1068 source : AC8 34) chain L residue 19 type sequence C description BINDING SITE FOR RESIDUE ZN L 1059 source : AC9 35) chain L residue 22 type sequence C description BINDING SITE FOR RESIDUE ZN L 1059 source : AC9 36) chain L residue 24 type sequence T description BINDING SITE FOR RESIDUE ZN L 1059 source : AC9 37) chain L residue 36 type sequence C description BINDING SITE FOR RESIDUE ZN L 1059 source : AC9 38) chain L residue 39 type sequence C description BINDING SITE FOR RESIDUE ZN L 1059 source : AC9 39) chain A residue 154 type MOD_RES sequence C description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828 source Swiss-Prot : SWS_FT_FI1 40) chain A residue 1421 type MOD_RES sequence R description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828 source Swiss-Prot : SWS_FT_FI1 41) chain J residue 45 type MOD_RES sequence C description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828 source Swiss-Prot : SWS_FT_FI1 42) chain C residue 32-72 type prosite sequence NSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLI P description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSIRRvfiaevpiiAidwVqidaNsSvlhDEfIAhRLGLIP source prosite : PS00446 43) chain K residue 35-66 type prosite sequence INKEDHTLGNIIKSQLLKDPQVLFAGYKVPHP description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP source prosite : PS01154 44) chain B residue 932-944 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 45) chain E residue 142-155 type prosite sequence HELVPEHVVMTKEE description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPEHvvMtkEE source prosite : PS01110 46) chain F residue 58-72 type prosite sequence TKYERARVLGTRALQ description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARvLGtRAlQ source prosite : PS01111 47) chain I residue 112-118 type prosite sequence YVCTAPH description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH source prosite : PS00290 48) chain I residue 86-123 type prosite sequence CQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRW description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW source prosite : PS00466 49) chain I residue 16-42 type prosite sequence FCQECNNMLYPKEDKENRILLYACRNC description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCqECNNMLypkedkenrillyaCrnC source prosite : PS01030 50) chain J residue 2-11 type prosite sequence IIPVRCFTCG description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPVrCFTCG source prosite : PS01112 51) chain A residue 27 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI7 52) chain A residue 217 type MOD_RES sequence S description Phosphoserine => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI7 53) chain A residue 71 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 54) chain A residue 499 type BINDING sequence D description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 55) chain A residue 1416 type BINDING sequence R description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 56) chain A residue 74 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 57) chain A residue 81 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 58) chain A residue 84 type BINDING sequence H description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 59) chain A residue 111 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 60) chain A residue 114 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 61) chain A residue 184 type BINDING sequence C description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 62) chain A residue 346 type BINDING sequence K description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 63) chain A residue 460 type BINDING sequence R description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI2 64) chain A residue 493 type BINDING sequence N description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 65) chain A residue 495 type BINDING sequence D description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 66) chain I residue 119 type BINDING sequence C description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 67) chain B residue 1085 type BINDING sequence R description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 68) chain B residue 1119 type BINDING sequence C description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 69) chain B residue 1122 type BINDING sequence C description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 70) chain B residue 1137 type BINDING sequence C description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 71) chain B residue 1140 type BINDING sequence C description BINDING => ECO:0000250|UniProtKB:P24928 source Swiss-Prot : SWS_FT_FI4 72) chain A residue 497 type BINDING sequence D description BINDING => ECO:0000250|UniProtKB:P04050 source Swiss-Prot : SWS_FT_FI5 73) chain A residue 358 type BINDING sequence R description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI3 74) chain I residue 20 type BINDING sequence C description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI3 75) chain I residue 39 type BINDING sequence C description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI3 76) chain I residue 42 type BINDING sequence C description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK source Swiss-Prot : SWS_FT_FI3

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