2025-05-07 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation_author em_admin _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2024-05-31 2025-04-02 2025-04-02 2025-05-07 Agence Nationale de la Recherche (ANR) ANR-20-CE44-0020-01 France Agence Nationale de la Recherche (ANR) ANR-16-CE11-0025 France Instruct-ERIC Center (Strasbourg Centre) 19348 France Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - sigma-B udocked conformation Brodolin K Blaise M RNA polymerase; sigma factor; SigB, stress response; -10 promoter element; promoter recognition; tuberculosis, TRANSCRIPTION Vishwakarma RK Marechal N Morichaud Z Blaise M Margeat E Brodolin K Single-stranded DNA drives sigma subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations. Nucleic Acids Res. UK 53 2025 40240004 doi:10.1093/nar/gkaf272 1362-4962 0389 NARHAD Afonine PV Poon BK Read RJ Sobolev OV Terwilliger TC Urzhumtsev A Adams PD Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 74 531 544 2018 29872004 doi:10.1107/S2059798318006551 2059-7983 Morichaud Z Trapani S Vishwakarma RK Chaloin L Lionne C Lai-Kee-Him J Bron P Brodolin K Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Nat Commun UK 14 484 2023 36717560 doi:10.1038/s41467-023-36113-y 2041-1723 Sudalaiyadum Perumal A Vishwakarma RK Hu Y Morichaud Z Brodolin K RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase. Nucleic Acids Res UK 46 10106 10118 2018 30102406 doi:10.1093/nar/gky714 1362-4962 0389 NARHAD 9fjs FULLOVERLAP RNA polymerase holoenzyme bound to -10 promoter element ssDNA oligo RNA polymerase holoenzyme bound to -10 promoter element ssDNA oligo 0 1 2 3 4 5 6 Mycobacterium tuberculosis H37Rv 0.406 DNA-directed RNA polymerase subunit alpha Mycobacterium tuberculosis H37Rv 0.037745328 2 Escherichia coli BL21(DE3) LEVO MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNL KSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIG RIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEV AGYDVATGTWSTEGAYDEQDYAETEQL P9WGZ1 2.7.7.6 DNA-directed RNA polymerase subunit beta Mycobacterium tuberculosis H37Rv 0.12960234399999998 1 Escherichia coli BL21(DE3) LEVO MVLADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVG GLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKG TFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWT SEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERM TTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMC PIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVA EESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIM PWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVG KVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDK LAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELL EAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHAR STGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVL LKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA P9WGY9 2.7.7.6 DNA-directed RNA polymerase subunit beta' Mycobacterium tuberculosis H37Rv 0.147438344 1 Escherichia coli BL21(DE3) LEVO VNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVT RAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVE DQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRE LVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPE LRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLS DLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQV WDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSN NILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPP VEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYW ATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIV DSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQD VIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVR SVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGK APIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLR VQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAG RPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAY TIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYRHHHHHH P9WGY7 2.7.7.6 DNA-directed RNA polymerase subunit omega Mycobacterium tuberculosis H37Rv 0.01185114 1 Escherichia coli BL21(DE3) LEVO MSISQSDASLAAVPAVDQFDPSSGASGGYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNQLGEGILEYVG PLVEPGLQEKPLSIALREIHADLLEHTEGE P9WGY5 2.7.7.6 RNA polymerase sigma factor SigB Mycobacterium tuberculosis H37Rv 0.038572773
Addition of twenty N-terminal residues (MGSSHHHHHHSSGLVPRGSH) including 6xHIS tag
1 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSSGLVPRGSHMADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEH LLETRKRLGENRKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLLEHSRDPVSLDM PVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQ IERDVMSKLRHGERADRLRSYAS P9WGI5 DNA (17-MER) Escherichia coli 0.005297444
synthetic oligonucleotide
1 (DT)(DG)(DC)(DG)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DG)(DA) DNA ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 6 7.9 20.0 C8H18N2O4S HEPES 150.0 KCl potassium chloride 5.0 MgCl2 magnesium chloride 2.0 C4H10O2S2 dithiothreitol
8 mM CHAPSO added before vitrificaion
 Quantifoil R2/2 GOLD 200 PLASMA CLEANING ETHANE 90 291.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.01 0.8 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 9202 1.997 55.735
images were collected in super-resolution mode
 1 695496 cryoSPARC 3.3 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 FOURIER SPACE 3.48 FSC 0.143 CUT-OFF cryoSPARC 3.3 67957 MAXIMUM LIKELIHOOD cryoSPARC 3.3 MAXIMUM LIKELIHOOD cryoSPARC 3.3 cryoSPARC 3.3 emd_50511.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.5259665 0.978114 0.002375959 0.025733074 0.86200005 0.86200005 0.86200005 0.115 AUTHOR primary map 7PP4 PDB experimental model f 159-323 AlphaFold in silico model RIGID BODY FIT REAL emd_50511_msk_1.map emd_50511_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.12318326 0.4290864 0.002375959 0.016677683 0.86200005 0.86200005 0.86200005 AUTHOR Raw map emd_50511_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.34331977 0.60757077 0.00165944 0.045626976 0.86200005 0.86200005 0.86200005 AUTHOR half-map B emd_50511_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.3404346 0.6166905 0.0016534461 0.045673408 0.86200005 0.86200005 0.86200005 AUTHOR half-map A