7KUG | pdb_00007kug

Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.200 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KUG

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis.

Wan, T.Horova, M.Beltran, D.G.Li, S.Wong, H.X.Zhang, L.M.

(2021) Mol Cell 81: 2887

  • DOI: https://doi.org/10.1016/j.molcel.2021.06.002
  • Primary Citation Related Structures: 
    7KUF, 7KUG

  • PubMed Abstract: 

    WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σ A 4 ) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σ A 4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σ A 4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σ A 4 -bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.


  • Organizational Affiliation
    • Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.

Macromolecule Content 

  • Total Structure Weight: 43.86 kDa 
  • Atom Count: 2,859 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 382 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable transcriptional regulator WhiB7
A, C
79Mycobacterium tuberculosis H37RvMutation(s): 2 
Gene Names: whiB7Rv3197ARv3197.1
UniProt
Find proteins for Q6MX01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q6MX01 
Go to UniProtKB:  Q6MX01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MX01
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera
B, D
112Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigAERS007670_01286ERS007681_03833ERS007688_01862
EC: 2.7.7.6
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGI1 
Go to UniProtKB:  P9WGI1
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY9 
Go to UniProtKB:  P9WGY9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP9WGY9P9WGI1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.200 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.586α = 90
b = 61.028β = 90
c = 210.225γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2562300224001
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM138157-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM113126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM103335

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary