6F6W

Structure of Mycobacterium smegmatis RNA polymerase core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Core and Holoenzyme Forms of RNA Polymerase fromMycobacterium smegmatis.

Kouba, T.Pospisil, J.Hnilicova, J.Sanderova, H.Barvik, I.Krasny, L.

(2019) J Bacteriol 201

  • DOI: 10.1128/JB.00583-18
  • Primary Citation of Related Structures:  
    6F6W, 6EYD

  • PubMed Abstract: 
  • Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σ A but no other factors ...

    Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σ A but no other factors. Each form was detected by cryo-electron microscopy in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme and confirm that region 1.1 of σ A is directed into the primary channel of RNAP. Taken together, we describe the conformational changes of unrestrained mycobacterial RNAP. IMPORTANCE We describe here three-dimensional structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-electron microscopy. These structures fill the thus-far-empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.


    Organizational Affiliation

    Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic tkouba@embl.fr krasny@biomed.cas.cz.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoAMSMEG_1524MSMEI_1488
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1178Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoBMSMEG_1367MSMEI_1328
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1325Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoCMSMEG_1368MSMEI_1329
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZMSMEG_3053MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QWT1 
Go to UniProtKB:  A0QWT1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth D], G [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other