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Open data
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Basic information
Entry | Database: PDB / ID: 6c06 | ||||||
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Title | Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin | ||||||
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![]() | transcription/antibiotic / initiation / antibiotic / switch region inhibitor / TRANSCRIPTION / transcription-antibiotic complex | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.15 Å | ||||||
![]() | Darst, S.A. / Campbell, E.A. / 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, S.A. / Campbell, E.A. / Boyaci Selcuk, H. / Chen, J. / Lilic, M. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 629.8 KB | Display | ![]() |
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PDB format | ![]() | 479.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 314.2 KB | Display | |
Data in CIF | ![]() | 429.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7323MC ![]() 7319C ![]() 7320C ![]() 7322C ![]() 6bzoC ![]() 6c04C ![]() 6c05C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rpoA, rpoA_1, CLD25_18970, ERS007661_01801, ERS007663_01917, ERS007665_01054, ERS007670_00938, ERS007672_03180, ERS007679_01858, ERS007688_02121, ERS007703_04392, ERS007720_00529, ERS007722_ ...Gene: rpoA, rpoA_1, CLD25_18970, ERS007661_01801, ERS007663_01917, ERS007665_01054, ERS007670_00938, ERS007672_03180, ERS007679_01858, ERS007688_02121, ERS007703_04392, ERS007720_00529, ERS007722_04215, ERS023446_02770, ERS024213_02470, ERS027644_00781, ERS027646_02177, ERS027652_00409, ERS027653_00362, ERS027654_02191, ERS027656_00886, ERS027659_01235, ERS027661_02549, ERS027666_01143, ERS124361_03550, SAMEA2682864_03600, SAMEA2683035_02863 Production host: ![]() ![]() References: UniProt: A0A045J8T1, UniProt: P9WGZ1*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 130198.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: V9Z879, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 148074.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rpoC, rpoC_1, CLD25_03785, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, SAMEA2682864_01702 Production host: ![]() ![]() References: UniProt: A0A045J9E2, UniProt: P9WGY7*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 11776.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 Production host: ![]() ![]() References: UniProt: A0A0T9N9K3, UniProt: P9WGY5*PLUS, DNA-directed RNA polymerase |
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-Protein , 2 types, 2 molecules FJ
#5: Protein | Mass: 58169.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: sigA, hrdB_2, CLD25_14885, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS023446_01203, ERS024213_00371, ERS024276_00878, ERS027644_01437, ERS027646_01351, ERS027653_ ...Gene: sigA, hrdB_2, CLD25_14885, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS023446_01203, ERS024213_00371, ERS024276_00878, ERS027644_01437, ERS027646_01351, ERS027653_01295, ERS027661_00252, ERS124361_02215, SAMEA2682864_02073, SAMEA2683035_01696 Production host: ![]() ![]() |
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#6: Protein | Mass: 12993.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rbpA, CLD25_11245, ERS007670_01223, ERS007672_02518, ERS007679_02287, ERS007681_03389, ERS007688_02707, ERS007703_03544, ERS007720_03893, ERS007722_02881, ERS007731_02971, ERS007739_00749, ...Gene: rbpA, CLD25_11245, ERS007670_01223, ERS007672_02518, ERS007679_02287, ERS007681_03389, ERS007688_02707, ERS007703_03544, ERS007720_03893, ERS007722_02881, ERS007731_02971, ERS007739_00749, ERS007741_03837, ERS023446_04025, ERS024213_00234, ERS024276_03708, ERS027644_04191, ERS027646_02841, ERS027652_02278, ERS027653_01824, ERS027654_04301, ERS027656_03007, ERS027659_00863, ERS027661_00907, ERS027666_04473, ERS031537_02569, ERS124361_01290, SAMEA2682864_00634, SAMEA2683035_00392 Production host: ![]() ![]() |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FI8.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FI8.gif)
#7: Chemical | #8: Chemical | ChemComp-MG / | #9: Chemical | ChemComp-FI8 / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mycobacterium tuberculosis RNAP Holo with RbpA and Fidaxomicin Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 6.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171547 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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