+Open data
-Basic information
Entry | Database: PDB / ID: 6c04 | ||||||
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Title | Mtb RNAP Holo/RbpA/double fork DNA -closed clamp | ||||||
Components |
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Keywords | transcription/dna / initiation / transcription bubble / closed clamp / TRANSCRIPTION / transcription-dna 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 / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | ||||||
Authors | Darst, S.A. / Campbell, E.A. / Boyaci Selcuk, H. / Chen, J. / Lilic, M. | ||||||
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, S.A. / Campbell, E.A. / Boyaci Selcuk, H. / Chen, J. / Lilic, M. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6c04.cif.gz | 651.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c04.ent.gz | 510.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/6c04 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/6c04 | HTTPS FTP |
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-Related structure data
Related structure data | 7320MC 7319C 7322C 7323C 6bzoC 6c05C 6c06C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (bacteria) / Gene: rpoA, rpoA_1, CLD25_18970 / Production host: Escherichia coli (E. coli) References: UniProt: A0A045J8T1, UniProt: P9WGZ1*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 130070.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoB, SAMEA2682864_01701 / Production host: Escherichia coli (E. coli) References: UniProt: V9Z879, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 148202.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoC, rpoC_1, CLD25_03785 / Production host: Escherichia coli (E. coli) 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.) Mycobacterium tuberculosis (bacteria) / Gene: rpoZ / Production host: Escherichia coli (E. coli) 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.) Mycobacterium tuberculosis (bacteria) / Gene: sigA, hrdB_2, CLD25_14885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045HD00, UniProt: P9WGI1*PLUS |
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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.) Mycobacterium tuberculosis (bacteria) / Gene: rbpA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IP01, UniProt: P9WHJ5*PLUS |
-DNA chain , 2 types, 4 molecules OHPG
#7: DNA chain | Mass: 9565.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) #8: DNA chain | Mass: 7930.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) |
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-Non-polymers , 2 types, 3 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / | |
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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 |
-Sample preparation
Component | Name: Mtb RNAP Holo/RbpA/double fork DNA / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 6.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171547 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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