6C06

Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts.

Boyaci, H.Chen, J.Lilic, M.Palka, M.Mooney, R.A.Landick, R.Darst, S.A.Campbell, E.A.

(2018) Elife 7

  • DOI: 10.7554/eLife.34823
  • Primary Citation of Related Structures:  
    6C04, 6C06, 6C05, 6BZO

  • PubMed Abstract: 
  • Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption ...

    Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile 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 M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis . Additional structures define conformational states of M. tuberculosis 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.


    Related Citations: 
    • Structure of Mycobacterium Tuberculosis RNAP Holo Enzyme/RbpA in closed clamp conformation
      Darst, S.A., Campbell, E.A., Boyaci Selcuk, H., Chen, J., Lilic, M.
      () To be published --: --

    Organizational Affiliation

    The Rockefeller University, New York, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha AB347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGZ1 
Go to UniProtKB:  P9WGZ1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta C1181Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoBSAMEA2682864_01701
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY9 
Go to UniProtKB:  P9WGY9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta' D1324Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoCrpoC_1CLD25_03785ERS007665_00591ERS023446_00410ERS031537_00289ERS124361_01694SAMEA2682864_01702
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY7 
Go to UniProtKB:  P9WGY7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega E110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoZERS007672_03979ERS007703_04032ERS007720_04749ERS027652_00548ERS027654_02543ERS027656_03959ERS124361_02246
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY5 
Go to UniProtKB:  P9WGY5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA F531Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGI1 
Go to UniProtKB:  P9WGI1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpA J111Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for P9WHJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHJ5 
Go to UniProtKB:  P9WHJ5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FI8
Query on FI8

Download Ideal Coordinates CCD File 
D
Fidaxomicin
C52 H74 Cl2 O18
ZVGNESXIJDCBKN-UUEYKCAUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release