5VI5

Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures.

Hubin, E.A.Lilic, M.Darst, S.A.Campbell, E.A.

(2017) Nat Commun 8: 16072-16072

  • DOI: 10.1038/ncomms16072
  • Primary Citation of Related Structures:  
    5VI8, 5VI5

  • PubMed Abstract: 
  • The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), alo ...

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A , which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.


    Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoAMSMEG_1524MSMEI_1488
EC: 2.7.7.6
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Go to UniProtKB:  A0QSL8
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoBMSMEG_1367MSMEI_1328
EC: 2.7.7.6
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoCMSMEG_1368MSMEI_1329
EC: 2.7.7.6
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZMSMEG_3053MSMEI_2977
EC: 2.7.7.6
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoDsigAMSMEG_2758MSMEI_2690
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAJ114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpAMSMEG_3858MSMEI_3768
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (49-MER)O50synthetic construct
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (44-MER)P50synthetic construct
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*CP*GP*A)-3')Q4synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.280 
    • R-Value Work: 0.253 
    • R-Value Observed: 0.254 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 132.062α = 90
    b = 163.555β = 107.9
    c = 139.964γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM114450

    Revision History 

    • Version 1.0: 2017-07-26
      Type: Initial release
    • Version 1.1: 2020-01-01
      Changes: Author supporting evidence