The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA

2026-04-15 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2025-07-07 2026-02-25 2026-02-25 2026-04-15 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM130290 United States The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Singh RR Schumacher MA CCNA_03891-CCNA_01149 promoter complex, DriD, Caulobacter, RNA Polymerase, Transcription, TRANSCRIPTION-DNA complex Singh RR Chinni A Cannistraci E Salinas R Yadav S Gozzi K Schumacher MA Transcription activation mechanism of a noncanonical DNA damage response pathway by the WYL-activator, DriD. Sci Adv US 12 eaec6337 eaec6337 2026 41861017 doi:10.1126/sciadv.aec6337 2375-2548 Singh RR Schumacher MA The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex To Be Published 0353 Singh RR Schumacher MA The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex To Be Published 0353 Singh RR Schumacher MA The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex To Be Published 0353 9pgh FULLOVERLAP EMDB EMD-71632 associated EM volume

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex 0 1 2 3 4 5 6 7 Caulobacter vibrioides NA1000 ML2315 (BSL1) DNA-directed RNA polymerase subunit alpha Caulobacter vibrioides NA1000 ML2315 (BSL1) 0.037315522999999996 2 LEVO MIERNWNELIRPEKPQIETGADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAVTAIQIDGVVHEFSSLEGVRED VVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIETPADIEILNPDHVLCTLDDGASVRMEFTVNNGKGYVPADRN RPEDAPIGLIAVDALYSPVKRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAKS ADESKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAGMGLHLGMDVP NWPPENIEDLAKKFEDQI Q9A8S9 2.7.7.6 DNA-directed RNA polymerase subunit beta Caulobacter vibrioides NA1000 ML2315 (BSL1) 0.15108560899999998 1 LEVO MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQRETRPGLRRDEGVEAVFKSVFPIKDFNERAVLEYVSYEFE EPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPG VFFDHDKGKTHASGKLLFAARVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRS GGWATPYKPERWRGVKPEFPLVDADTGEEVAPAGTKITARQAKKFADGGLKTLLLAPEALTGRYLARDAVNMATGEIYAE AGDELDVTSIQALADQGFSTIDVLDIDHVTVGAYMRNTLRVDKNAIREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDA ERYDLSSVGRVKMNMRLEQDVSDEVRILRKEDVLAVLKVLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRME RAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHP THYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPYRRVKDGKPQDEVVYMSAMEESKHVIAQSNIKVAEGEIVEDL VPGRINGEPTLLQKETVDLMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAVVARDSG AVVIAKRTGVVEQIDGTRIVIRATEETDPARSGVDIYRMSKFQRSNQSTCINQRPLVKVGDRIVAGDIIADGPSTELGEL ALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIG AEVQPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALAIERAEID RLGKDRDDEFAILNRNISGRLKELLIGKVALSGPKGLSRGEITAEGLAQVASGLWWQIALEDEKAMGELESLRRLFDENR KRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLG VPSRMNVGQIFETHLGWACANLGKQITNLLEDWQQGGQKQALVERLTEIYGPDEELPDTEEGLVELARNLGKGVPIATPV FDGARMDDIEGHLEMAGVNKSGQSILFDGLTGEQFKRPVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFG GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS Q9AAU2 2.7.7.6 DNA-directed RNA polymerase subunit beta' Caulobacter vibrioides NA1000 ML2315 (BSL1) 0.154467 1 LEVO MNQEVLNIFNPVQAAPTFDQIRISLASPEKIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPTKDYECLCGKYKRMK YKGIICEKCGVEVTLARVRRERMGHIELASPVAHIWFLKSLPSRIAMMLDMPLKDIERVLYFEYYIVTEPGLTPLKQHQL LSEDDYMRAQEEYGDDSFTAEIGAEAIQNLLKAIDLEKEAERLREELSGTVSDMKQKKFSKRLKILEAFQESGNRPEWMV LTVVPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPDIIIRNEKRMLQESVDALFDNGRRGRVITG ANKRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHECGLPKKMALELFKPFIYARLDAKGLSGTVKQSK RMVEREQPQVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPKLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSLEAQL EARVLMMSTNNILSPANGRPIIVPSQDIVLGLYYLSVARDGEPGEGKIFADLGEIEAAMDAGVVSLHAKIKARHTEMTPE GVLLRKVIDTTPGRMKIAALLPHHPQIGHRLIEKALTKKEIGNLIDIVYRHCGQKATVIFADKVMGLGFKEAAKAGISFG KDDIIIPVRKTAIVEETRKLAEEYEQQYADGLITKGEKYNKVVDAWAKATDRVADEMMAELQMKHKDENGREKEINAIYM MAHSGARGSQAQMKQLGGMRGLMAKPSGEIIETPIVSNFKEGLTVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVA QDCIIVEEDCGTTKGITLRAVVEGGDVLVSLGSRVLGRFTAEDVKDPGTGELVVPADTYIDENIADAIEAAVVQSVKVRS VLTCEAKIGVCGACYGRDLARGTPVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGTAQVAEQSFFEASNEGTVRVIGPTV VGSDGALVIMSRNTSVSVLVDGKERETYKPPYGARLRVKDGDLVKRGQRLGDWDPYTTPIITEVAGKIRAEDLVDGLSIR EEVDEATGIAQRVVADWRTSARGSDLRPAMGVLSEDGSYKRLSNGGEARYLLSAGAILSVADGDEVKPGEVIARIPTEGA KTRDITGGLPRVAELFEARRPKDCAVIAEMDGRVEFGKDYKNKRRIKITPDVDADGNQPEAVEFLIPKGKHIAVHDGDYI TKGEYIIDGNPDPHDILRILGVEALANFLVDEIQEVYRLQGVPINDKHIETIVRQMLQKVEILEPGDTGLIKGDHLDKPE FDKEQEKAIARGGRPAVTQPVLLGITKASLQTKSFISAASFQETTRVLTEASVHGKTDTLEGLKENVIVGRLIPAGTGSY LRSLQRVAAKRDEQLAQQREDAMEPLPAEIALSDAE Q9AAU1 2.7.7.6 DNA-directed RNA polymerase subunit omega Caulobacter vibrioides NA1000 ML2315 (BSL1) 0.013289843999999999 1 LEVO MARVTVEDCVEKVPNRFALVLLSAHRARGISAGAALMVDRDNDKNPVVALREIADDVIDHEGLKEHLISTLQRVDEHTEA EEEAETLALLADPSHMQMSELELVRALQSDRDGGQEERY P58066 2.7.7.6 RNA polymerase sigma factor RpoD Caulobacter vibrioides NA1000 ML2315 (BSL1) 0.07277017200000001 1 Escherichia coli BL21(DE3) LEVO MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEE DAENAEGGEVATRDENTTVIASDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEA IMVWREELGTGRILLREVIDLEGTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEG ELREGVMAILDAIASEFEAFRKLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRL IGLEGRLLRLADSYGISRGEFLKAYFGSELNPTWSEQVKAMGVRWTKFVENDSQSVTDIRSEIAALATETGVPIDDYRRI VQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR SIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD FIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHP SRSRKLRSFLDS P52324 DNA (55-MER)-non template Caulobacter vibrioides NA1000 0.030196248 1 (DC)(DA)(DT)(DG)(DC)(DC)(DG)(DC)(DC)(DC)(DG)(DT)(DC)(DA)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DG)(DT)(DT)(DT)(DC)(DT)(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DT)(DG)(DC)(DG)(DC)(DG) (DG)(DA)(DC)(DA)(DA)(DT)(DC)(DT)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DT)(DC)(DG)(DC)(DC) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DG)(DA)(DC)(DC)(DT) (DT)(DC)(DG)(DA)(DT)(DG)(DA)(DC)(DC)(DC)(DG)(DC)(DT)(DT)(DC)(DG)(DC)(DC)(DT) CP001340.1 DNA DNA (43-MER)-template Caulobacter vibrioides NA1000 0.030894679999999997 1 (DA)(DG)(DG)(DC)(DG)(DA)(DA)(DG)(DC)(DG)(DG)(DG)(DT)(DC)(DA)(DT)(DC)(DG)(DA)(DA) (DG)(DG)(DT)(DC)(DC)(DT)(DT)(DG)(DG)(DG)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DG) (DG)(DC)(DG)(DA)(DT)(DG)(DA)(DT)(DG)(DG)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DT)(DC)(DC) (DG)(DC)(DG)(DC)(DA)(DT)(DT)(DG)(DC)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA)(DC)(DG)(DG) (DT)(DC)(DG)(DT)(DA)(DT)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DG)(DG)(DC)(DA)(DT)(DG) CP001340.1 DNA MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 1.5 8.0 20.0 C4H11NO3 Tris-HCl 5.0 MgCl2 Magnesium Chloride 100.0 NaCl Sodium Chloride 1.0 C2H6OS 1

20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME

UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 50.0 GLOW DISCHARGE 300 AIR ETHANE 90 293.15 LEICA EM GP

3 uM of the reconstituted complex

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.8 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 58.7 1 cryoSPARC 4.2.1 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-Initio Reconstruction

C1 3.54 FSC 0.143 CUT-OFF RELION 5 150644 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD RELION 5 emd_71632.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.72003 414.72003 414.72003 90.0 90.0 90.0 X Y Z -0.034164384 0.07076755 0.000022486021 0.001341611 1.08 1.08 1.08 0.0033 AUTHOR ::::EMDATABANK.org::::EMD-71632:::: 7ye1 PDB experimental model emd_71632_msk_1.map emd_71632_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.72003 414.72003 414.72003 90.0 90.0 90.0 X Y Z -0.017562583 0.042943366 0.000022493323 0.001811744 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-71632:::: emd_71632_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.72003 414.72003 414.72003 90.0 90.0 90.0 X Y Z -0.01609908 0.042646453 0.000022478718 0.0018076263 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-71632::::