4NQW | pdb_00004nqw

Structure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigK in complex with the cytosolic domain of its cognate anti-sigma factor RskA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.260 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4NQW

This is version 1.2 of the entry. See complete history

Literature

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex

Shukla, J.Gupta, R.Thakur, K.G.Gokhale, R.Gopal, B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1026-1036

  • DOI: https://doi.org/10.1107/S1399004714000121
  • Primary Citation Related Structures: 
    4NQW

  • PubMed Abstract: 

    The host-pathogen interactions in Mycobacterium tuberculosis infection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracytoplasmic function (ECF) σ factor σ(K) governs the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of σ(K) are regulated by the membrane-associated anti-σ(K) (RskA) that localizes σ(K) in an inactive complex. The crystal structure of M. tuberculosis σ(K) in complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the -35 promoter-interaction region of σ(K). Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in σ(K) is consistent with its role as a sensor. The disulfide bond in σ(K) influences the stability of the σ(K)-RskAcyto complex but does not interfere with σ(K)-promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecule Content 

  • Total Structure Weight: 32.65 kDa 
  • Atom Count: 1,849 
  • Modeled Residue Count: 221 
  • Deposited Residue Count: 284 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ECF RNA polymerase sigma factor SigK204Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv0445csigK
UniProt
Find proteins for P9WGH7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGH7 
Go to UniProtKB:  P9WGH7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGH7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-sigma-K factor RskA80Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rskARv0444c
UniProt
Find proteins for P9WGX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGX5 
Go to UniProtKB:  P9WGX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGX5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.260 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.39α = 90
b = 57.39β = 90
c = 150.87γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary