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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7322 | |||||||||
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Title | Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state | |||||||||
![]() | primary map | |||||||||
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Function / homology | ![]() bacterial-type RNA polymerase holo enzyme binding / response to water / Antimicrobial action and antimicrobial resistance in Mtb / bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...bacterial-type RNA polymerase holo enzyme binding / response to water / Antimicrobial action and antimicrobial resistance in Mtb / bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / protein dimerization activity / response to antibiotic / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.15 Å | |||||||||
![]() | Darst SA / Campbell EA / Boyaci Selcuk H / Chen J / Lilic M | |||||||||
![]() | ![]() Title: Fidaxomicin jams RNA polymerase motions needed for initiation via RbpA contacts. Authors: Hande Boyaci / James Chen / Mirjana Lilic / Margaret Palka / Rachel Anne Mooney / Robert Landick / Seth A Darst / Elizabeth A Campbell / ![]() Abstract: Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor ...Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on . Additional structures define conformational states of RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket. #1: ![]() Title: Structure of Mycobacterium Tuberculosis RNAP Holo Enzyme/RbpA in closed clamp conformation Authors: Darst SA / Campbell EA / Boyaci Selcuk H / Chen J / Lilic M | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
Images | ![]() | 144.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c05MC ![]() 7319C ![]() 7320C ![]() 7323C ![]() 6bzoC ![]() 6c04C ![]() 6c06C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mycobacterium tuberculosis RNAP Holo with RbpA
Entire | Name: Mycobacterium tuberculosis RNAP Holo with RbpA |
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Components |
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-Supramolecule #1: Mycobacterium tuberculosis RNAP Holo with RbpA
Supramolecule | Name: Mycobacterium tuberculosis RNAP Holo with RbpA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: DNA-directed RNA polymerase subunit alpha
Macromolecule | Name: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.745328 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY ...String: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY SPVLKVTYKV DATRVEQRTD FDKLILDVET KNSISPRDAL ASAGKTLVEL FGLARELNVE AEGIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPPSFDP SEV AGYDVA TGTWSTEGAY DEQDYAETEQ L |
-Macromolecule #2: DNA-directed RNA polymerase subunit beta
Macromolecule | Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 130.198922 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV ...String: MADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV VVSQLVRSPG VYFDETIDKS TDKTLHSVKV IPSRGAWLEF DVDKRDTVGV RIDRKRRQPV TVLLKALGWT SE QIVERFG FSEIMRSTLE KDNTVGTDEA LLDIYRKLRP GEPPTKESAQ TLLENLFFKE KRYDLARVGR YKVNKKLGLH VGE PITSST LTEEDVVATI EYLVRLHEGQ TTMTVPGGVE VPVETDDIDH FGNRRLRTVG ELIQNQIRVG MSRMERVVRE RMTT QDVEA ITPQTLINIR PVVAAIKEFF GTSQLSQFMD QNNPLSGLTH KRRLSALGPG GLSRERAGLE VRDVHPSHYG RMCPI ETPE GPNIGLIGSL SVYARVNPFG FIETPYRKVV DGVVSDEIVY LTADEEDRHV VAQANSPIDA DGRFVEPRVL VRRKAG EVE YVPSSEVDYM DVSPRQMVSV ATAMIPFLEH DDANRALMGA NMQRQAVPLV RSEAPLVGTG MELRAAIDAG DVVVAEE SG VIEEVSADYI TVMHDNGTRR TYRMRKFARS NHGTCANQCP IVDAGDRVEA GQVIADGPCT DDGEMALGKN LLVAIMPW E GHNYEDAIIL SNRLVEEDVL TSIHIEEHEI DARDTKLGAE EITRDIPNIS DEVLADLDER GIVRIGAEVR DGDILVGKV TPKGETELTP EERLLRAIFG EKAREVRDTS LKVPHGESGK VIGIRVFSRE DEDELPAGVN ELVRVYVAQK RKISDGDKLA GRHGNKGVI GKILPVEDMP FLADGTPVDI ILNTHGVPRR MNIGQILETH LGWCAHSGWK VDAAKGVPDW AARLPDELLE A QPNAIVST PVFDGAQEAE LQGLLSCTLP NRDGDVLVDA DGKAMLFDGR SGEPFPYPVT VGYMYIMKLH HLVDDKIHAR ST GPYSMIT QQPLGGKAQF GGQRFGEMEC WAMQAYGAAY TLQELLTIKS DDTVGRVKVY EAIVKGENIP EPGIPESFKV LLK ELQSLC LNVEVLSSDG AAIELREGED EDLERAAANL GINLSRNESA SVEDLALARH GGSGA |
-Macromolecule #3: DNA-directed RNA polymerase subunit beta'
Macromolecule | Name: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 148.074094 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLDVNFFDEL RIGLATAEDI RQWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DEEMRHNELS TLEAEMAVER K AVEDQRDG ...String: MLDVNFFDEL RIGLATAEDI RQWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DEEMRHNELS TLEAEMAVER K AVEDQRDG ELEARAQKLE ADLAELEAEG AKADARRKVR DGGEREMRQI RDRAQRELDR LEDIWSTFTK LAPKQLIVDE NL YRELVDR YGEYFTGAMG AESIQKLIEN FDIDAEAESL RDVIRNGKGQ KKLRALKRLK VVAAFQQSGN SPMGMVLDAV PVI PPELRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LIDLGAPEII VNNEKRMLQE SVDALFDNGR RGRPVTGPGN RPLK SLSDL LKGKQGRFRQ NLLGKRVDYS GRSVIVVGPQ LKLHQCGLPK LMALELFKPF VMKRLVDLNH AQNIKSAKRM VERQR PQVW DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP MLVEGKAIQL HPLVCEAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILSPASGRP LAMPRLDMVT GLYYLTTEVP GDTGEYQPAS GDHPETGVYS SPAEAIMAAD RGVLSVRAKI KVRLTQL RP PVEIEAELFG HSGWQPGDAW MAETTLGRVM FNELLPLGYP FVNKQMHKKV QAAIINDLAE RYPMIVVAQT VDKLKDAG F YWATRSGVTV SMADVLVPPR KKEILDHYEE RADKVEKQFQ RGALNHDERN EALVEIWKEA TDEVGQALRE HYPDDNPII TIVDSGATGN FTQTRTLAGM KGLVTNPKGE FIPRPVKSSF REGLTVLEYF INTHGARKGL ADTALRTADS GYLTRRLVDV SQDVIVREH DCQTERGIVV ELAERAPDGT LIRDPYIETS AYARTLGTDA VDEAGNVIVE RGQDLGDPEI DALLAAGITQ V KVRSVLTC ATSTGVCATC YGRSMATGKL VDIGEAVGIV AAQSIGEPGT QLTMRTFHQG GVGEDITGGL PRVQELFEAR VP RGKAPIA DVTGRVRLED GERFYKITIV PDDGGEEVVY DKISKRQRLR VFKHEDGSER VLSDGDHVEV GQQLMEGSAD PHE VLRVQG PREVQIHLVR EVQEVYRAQG VSIHDKHIEV IVRQMLRRVT IIDSGSTEFL PGSLIDRAEF EAENRRVVAE GGEP AAGRP VLMGITKASL ATDSWLSAAS FQETTRVLTD AAINCRSDKL NGLKENVIIG KLIPAGTGIN RYRNIAVQPT EEARA AAYT IPSYEDQYYS PDFGAATGAA VPLDDYGYSD YRHHHHHHHH |
-Macromolecule #4: DNA-directed RNA polymerase subunit omega
Macromolecule | Name: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.776996 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQE KPLSIALREI HADLLEHTEG E |
-Macromolecule #5: RNA polymerase sigma factor SigA
Macromolecule | Name: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 58.169477 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPHMAATKAS TATDEPVKRT ATKSPAASAS GAKTGAKRTA AKSASGSPPA KRATKPAARS VKPASAPQDT TTSTIPKRKT RAAAKSAAA KAPSARGHAT KPRAPKDAQH EAATDPEDAL DSVEELDAEP DLDVEPGEDL DLDAADLNLD DLEDDVAPDA D DDLDSGDD ...String: GPHMAATKAS TATDEPVKRT ATKSPAASAS GAKTGAKRTA AKSASGSPPA KRATKPAARS VKPASAPQDT TTSTIPKRKT RAAAKSAAA KAPSARGHAT KPRAPKDAQH EAATDPEDAL DSVEELDAEP DLDVEPGEDL DLDAADLNLD DLEDDVAPDA D DDLDSGDD EDHEDLEAEA AVAPGQTADD DEEIAEPTEK DKASGDFVWD EDESEALRQA RKDAELTASA DSVRAYLKQI GK VALLNAE EEVELAKRIE AGLYATQLMT ELSERGEKLP AAQRRDMMWI CRDGDRAKNH LLEANLRLVV SLAKRYTGRG MAF LDLIQE GNLGLIRAVE KFDYTKGYKF STYATWWIRQ AITRAMADQA RTIRIPVHMV EVINKLGRIQ RELLQDLGRE PTPE ELAKE MDITPEKVLE IQQYAREPIS LDQTIGDEGD SQLGDFIEDS EAVVAVDAVS FTLLQDQLQS VLDTLSEREA GVVRL RFGL TDGQPRTLDE IGQVYGVTRE RIRQIESKTM SKLRHPSRSQ VLRDYLD |
-Macromolecule #6: RNA polymerase-binding protein RbpA
Macromolecule | Name: RNA polymerase-binding protein RbpA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.993695 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADRVLRGSR LGAVSYETDR NHDLAPRQIA RYRTDNGEEF EVPFADDAEI PGTWLCRNGM EGTLIEGDLP EPKKVKPPRT HWDMLLERR SIEELEELLK ERLELIRSRR RG |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 6.7 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171547 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |