2024-05-15 REL PDBe PDBe PDBe 2017-12-19 2018-02-28 2018-02-28 2024-05-15 Rega Foundation Belgium Single particle cryo em structure of Mycobacterium tuberculosis RNA polymerase in complex with Fidaxomicin Das K Lipiarmycin, RNA pol, RNAP, inhibitor, drug, Clostridium difficile, ANTIBIOTIC, Tiacumicin B, CCDC 114782, transcription Lin W Das K Degen D Mazumder A Duchi D Wang D Ebright YW Ebright RY Sineva E Gigliotti M Srivastava A Mandal S Jiang Y Liu Y Yin R Zhang Z Eng ET Thomas D Donadio S Zhang H Zhang C Kapanidis AN Ebright RH Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Mol. Cell US 70 60 71.e15 2018 29606590 doi:10.1016/j.molcel.2018.02.026 1097-4164 2168 MOCEFL 6fbv FULLOVERLAP structure of Mycobacterium tuberculosis RNA polymerase in complex with Fidaxomicin structure of Mycobacterium tuberculosis RNA polymerase in complex with Fidaxomicin 0 1 2 3 4 5
RNA polymerase inhibitor complex
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) DNA-directed RNA polymerase subunit alpha Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 0.037745328 2 Escherichia coli LEVO MLLSQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNL KSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIG RIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEV AGYDVATGTWSTEGAYDEQDYAETEQL P9WGZ1 2.7.7.6 DNA-directed RNA polymerase subunit beta Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 0.13001882799999998 1 Escherichia coli LEVO MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDV NPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMM TEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKA LGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKL GLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVV RERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHY GRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVL VRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGD VVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLL VAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGD ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKIS DGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLP DELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDK IHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPES FKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA P9WGY9 2.7.7.6 DNA-directed RNA polymerase subunit beta' Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 0.146968969 1 Escherichia coli LEVO MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGV EVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERK AVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENL YRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVI PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLK SLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQR PQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILML SSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQL RPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAG FYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPII TIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDV SQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQV KVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVP RGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHE VLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEP AAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARA AAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYR P9WGY7 2.7.7.6 DNA-directed RNA polymerase subunit omega Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 0.01185114 1 Escherichia coli LEVO MSISQSDASLAAVPAVDQFDPSSGASGGYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNQLGEGILEYVG PLVEPGLQEKPLSIALREIHADLLEHTEGE P9WGY5 2.7.7.6 RNA polymerase sigma factor SigA Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 0.057877160000000004 1 Escherichia coli LEVO MAATKASTATDEPVKRTATKSPAASASGAKTGAKRTAAKSASGSPPAKRATKPAARSVKPASAPQDTTTSTIPKRKTRAA AKSAAAKAPSARGHATKPRAPKDAQHEAATDPEDALDSVEELDAEPDLDVEPGEDLDLDAADLNLDDLEDDVAPDADDDL DSGDDEDHEDLEAEAAVAPGQTADDDEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVAL LNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDL IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELA KEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFG LTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD P9WGI1 ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG Fidaxomicin 0.001058039 1 FI8 water 1.8015e-05 3 HOH singleParticle particle 8.0
3.5 microliter 1 microM Mtb RNAP-Lpm and 50 microMolar Lpm in 20 mM Tris-HCl, pH 8.0, 75 mM NaCl, 5 mM MgCl2, 5 mM dithiothreitol, and 0.1% n-octyl-beta-D-glucopyranoside
 COPPER 300 CARBON LACEY 100.0 GLOW DISCHARGE AIR 0.039 ETHANE 95 291 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 -0.001 -0.002 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-35 2 2458 0.2 1.4
Movies were recorded at 200 ms/frame for 10s (50 frames total), resulting in a total radiation dose of 72.05 electrons/A**2 per movie Defocus range was varied between 1.0 - 2.0 micrometer.
 1 819506
Autopick
 5UH5
Protein atoms only from the structure 5UH5; 60 A lowpass filter applied.
 C1 3.52 FSC 0.143 CUT-OFF RELION 2.0.5 68895 ANGULAR RECONSTITUTION RELION 2.0.5 ANGULAR RECONSTITUTION RELION 2.0.5 RELION 2.0.5 emd_4230.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 203.712 203.712 203.712 90.0 90.0 90.0 X Y Z -0.15635955 0.2548963 0.0016079389 0.012585061 1.061 1.061 1.061 0.03 AUTHOR OTHER Cross-correlation coefficient 95.299999999999997 emd_4230_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 254.64 254.64 254.64 90.0 90.0 90.0 X Y Z -0.022848621 0.051590845 0.0002275021 0.0033125908 1.061 1.061 1.061 AUTHOR emd_4230_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 254.64 254.64 254.64 90.0 90.0 90.0 X Y Z -0.024077551 0.052074816 0.00023065464 0.0034835683 1.061 1.061 1.061 AUTHOR