6FBV

Single particle cryo em structure of Mycobacterium tuberculosis RNA polymerase in complex with Fidaxomicin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

Lin, W.Das, K.Degen, D.Mazumder, A.Duchi, D.Wang, D.Ebright, Y.W.Ebright, R.Y.Sineva, E.Gigliotti, M.Srivastava, A.Mandal, S.Jiang, Y.Liu, Y.Yin, R.Zhang, Z.Eng, E.T.Thomas, D.Donadio, S.Zhang, H.Zhang, C.Kapanidis, A.N.Ebright, R.H.

(2018) Mol Cell 70: 60-71.e15

  • DOI: https://doi.org/10.1016/j.molcel.2018.02.026
  • Primary Citation of Related Structures:  
    6ASG, 6FBV

  • PubMed Abstract: 

    Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.


  • Organizational Affiliation

    Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoARv3457cMTCY13E12.10c
EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGZ1 
Go to UniProtKB:  P9WGZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGZ1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,178Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoBRv0667MTCI376.08c
EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGY9
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UniProt GroupP9WGY9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,316Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoCRv0668MTCI376.07c
EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGY7
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UniProt GroupP9WGY7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega110Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoZRv1390MTCY21B4.07
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY5 
Go to UniProtKB:  P9WGY5
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UniProt GroupP9WGY5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA528Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sigAmysArpoDrpoVRv2703MTCY05A6.24
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGI1 
Go to UniProtKB:  P9WGI1
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UniProt GroupP9WGI1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0.5
MODEL REFINEMENTPHENIX1.9

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Rega FoundationBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references, Refinement description