2024-05-22 REL PDBe PDBe PDBe 2020-05-11 2020-11-04 2020-11-04 2024-05-22 Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State III, primary channel dis-engaged and active site interfering Kouba T Koval T transcription cycle helicase-like protein RNA polymerase transcription, TRANSCRIPTION Kouba T Koval T Dohnalek J Krasny L HelD, a helicase-like protein from gram-positive bacteria in complex with RNA polymerase To Be Published 0353 EMD-10996 other EM volume 6z11 FULLOVERLAP Mycobacterium smegmatis HelD protein in complex with RNA polymerase core Mycobacterium smegmatis HelD protein in complex with RNA polymerase core 0 1 2 3 4 5 Mycolicibacterium smegmatis MC2 155 0.444 DNA-directed RNA polymerase subunit alpha Mycolicibacterium smegmatis MC2 155 0.037959441 2 Escherichia coli LEVO MLISQRPTLSEETVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNL KGLVVSSDDDEPVTMYLRKQGPGVVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIG RIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIIDVETKNSISPRDALASAGGTLVELFGLARELNADSEHIEIGPSPAE ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPATFDPSEV AGYDAATGTWTSDAGYDLDDNQDYAETEQL A0QSL8 2.7.7.6 DNA-directed RNA polymerase subunit beta Mycolicibacterium smegmatis MC2 155 0.128680141 1 Escherichia coli LEVO MLEGCILAVSSQSKSNAITNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEENPVGGLEEV LAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIIN GTERVVVSQLVRSPGVYFDETIDKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLNAGKPIT SSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDV EAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTDENGRFTEDRVMVRKKGGEVE FVSADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGV IEEVSADYITVMADDGTRQSYRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGH NYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPK GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKAGWNIDVAAGVPDWASKLPEELYSAPAD STVATPVFDGAQEGELAGLLGSTLPNRDGEVMVDADGKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPY SMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ SLCLNVEVLSSDGAAIEMRDGDDEDLERAAANLGINLSRNESASVEDLA P60281 2.7.7.6 DNA-directed RNA polymerase subunit beta' Mycolicibacterium smegmatis MC2 155 0.14671289099999998 1 Escherichia coli LEVO MLDVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGV EVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEAEMAVEKK AVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGEREMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVL YRELQDRYGEYFTGAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVI PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLK SLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQR PQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILML SSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTEL RPPTDLEAQLFENGWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPMIVVAQTVDKLKDAGF YWATRSGVTVSMADVLVPPQKQEILERHEAEADAIERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIIT IVKSGATGNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVS QDVIVREHDCETERGINVTLAERGPDGTLIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVK VRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVTGGADIVGGLPRVQELFEARV PRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVYDKLSKRQRLRVITHEDGTEGVLSDGDHVEVGDQLMEGAADPH EVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLTERAEFEAENRRVVAEGGE PAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEAR AAAYTIPSYEDQYYSPDFGQATGAAVPLDDYGYSDYR A0QS66 2.7.7.6 DNA-directed RNA polymerase subunit omega Mycolicibacterium smegmatis MC2 155 0.011544763 1 Escherichia coli LEVO MSTPHADAQLNAADDLGIDSSAASAYDTPLGITNPPIDELLSRASSKYALVIYAAKRARQINDYYNQLGDGILEYVGPLV EPGLQEKPLSIALREIHGDLLEHTEGE A0QWT1 2.7.7.6 RNA polymerase-associated transcription factor HelD Mycolicibacterium smegmatis MC2 155 0.081298078 1 Escherichia coli LEVO MSGRDYEDELQSERDYVAGLYARLDAERAQSQRRYAAALREHGGTAVERDAEVRALAKDIARLNVADNGLCFGRLDTLDD ARLYIGRLGIFDRDNDFEPLLLDWRAPMARPFYVATAANPENMRRRRQFHTLGRKVVDFTDEILGRPTGAEHDATNDAAL LAAVNAPRGEGMRDIVATIQAEQDQVIRLDHTGVLVIEGGPGTGKTVVALHRVAYLLYTYRKQMERHGVLVVGPTPAFLD HIGRVLPSLGESDAVFMTPGDFVPGLHVTAEDTPEAAEVKGSLKILDVLKAAVADRQELPSEPIPIDLSDVTMRIDAETA KWARDEARKTGLPHNEARAEFVDVVTYVVTERAVARIGRGWLTRDDKHAWEKMRADVVGELEDHEQFNAALDALWPILTP EDVLAQLYTSHERLRAAGAPECLWRADGEAWTVSDVPLLDELVDLLGRNKAADEAAERERREEEAYAAGVLDLMVDREDL MDDEDHLLAQDLIDAEELADRFKEQDNRELSERAAADREWTYGHVVVDEAQELSEMDWRLLMRRCPRRSFTIVGDLAQRR SPAGARSWGAMLDSYVPGRWVYKSLSVNYRTPAEIMAVAAAVLAEFAPDATPPDSVRACGVAPWARQVTDDDIASAIAEF VSEEAGREGTSVVIGPPDVPGTVPPSETKGLEFDAVLVVEPERILADGPRGAAELYVALTRATQRLGVLYRDALPQALAG LAEGDAAATVEQRTSA A0QUE0 3.6.4.12 ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.8 ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 50.0 1 6F6W 3.36 FSC 0.143 CUT-OFF RELION 3.1 119100 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION RELION emd_11026.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 299.19598 299.19598 299.19598 90.0 90.0 90.0 X Y Z -0.2623627 0.70966387 0.002057892 0.02382165 0.8310999 0.8310999 0.8310999 0.2 AUTHOR Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 3) 6F6W PDB experimental model 6VSX PDB experimental model AB INITIO MODEL emd_11026_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 299.19598 299.19598 299.19598 90.0 90.0 90.0 X Y Z -0.062931545 0.10069045 0.00007589769 0.004202025 0.8310999 0.8310999 0.8310999 AUTHOR Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 3) emd_11026_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 299.19598 299.19598 299.19598 90.0 90.0 90.0 X Y Z -0.035700787 0.06332607 0.00007587169 0.0041737743 0.8310999 0.8310999 0.8310999 AUTHOR Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (Halfmap 2) emd_11026_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 299.19598 299.19598 299.19598 90.0 90.0 90.0 X Y Z -0.04581452 0.060854103 0.00007592369 0.004303555 0.8310999 0.8310999 0.8310999 AUTHOR Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (Halfmap 1)