5VI8

Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1038/ncomms16072
  • Primary Citation of Related Structures:  
    5VI5, 5VI8

  • 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), 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAA [auth J]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpAMSMEG_3858MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QZ11
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth A],
C [auth B]
350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QSL8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth C]1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupP60281
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth D]1,317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth E]107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAG [auth F]466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoDsigAMSMEG_2758MSMEI_2690
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaJ [auth T]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (31-MER)H [auth O]31synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (26-MER)I [auth P]26synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth F]
K [auth C]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
K [auth C],
L [auth C],
M [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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P [auth D],
Q [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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EA [auth F]
N [auth C]
O [auth C]
W [auth D]
X [auth D]
EA [auth F],
N [auth C],
O [auth C],
W [auth D],
X [auth D],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.012α = 90
b = 161.633β = 107.72
c = 139.211γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description