+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7323 | |||||||||
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Title | Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin | |||||||||
Map data | primary map | |||||||||
Sample |
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Keywords | initiation / antibiotic / switch region inhibitor / TRANSCRIPTION / transcription-antibiotic complex | |||||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.15 Å | |||||||||
Authors | Darst SA / Campbell EA | |||||||||
Citation | Journal: Elife / Year: 2018 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: Journal: To Be Published 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7323.map.gz | 38 MB | EMDB map data format | |
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Header (meta data) | emd-7323-v30.xml emd-7323.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_7323.png | 121.3 KB | ||
Filedesc metadata | emd-7323.cif.gz | 8.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7323 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7323 | HTTPS FTP |
-Validation report
Summary document | emd_7323_validation.pdf.gz | 523.9 KB | Display | EMDB validaton report |
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Full document | emd_7323_full_validation.pdf.gz | 523.5 KB | Display | |
Data in XML | emd_7323_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | emd_7323_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7323 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7323 | HTTPS FTP |
-Related structure data
Related structure data | 6c06MC 7319C 7320C 7322C 6bzoC 6c04C 6c05C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7323.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
+Entire : Mycobacterium tuberculosis RNAP Holo with RbpA and Fidaxomicin
+Supramolecule #1: Mycobacterium tuberculosis RNAP Holo with RbpA and Fidaxomicin
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase sigma factor SigA
+Macromolecule #6: RNA polymerase-binding protein RbpA
+Macromolecule #7: ZINC ION
+Macromolecule #8: MAGNESIUM ION
+Macromolecule #9: Fidaxomicin
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171547 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |