9BIZ | pdb_00009biz

Crystal structure of the periplasmic domain of IgaA from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Molecular insights into the initiation step of the Rcs signaling pathway.

Watanabe, N.Savchenko, A.

(2024) Structure 32: 1381

  • DOI: https://doi.org/10.1016/j.str.2024.06.003
  • Primary Citation Related Structures: 
    9BIY, 9BIZ, 9BJ0

  • PubMed Abstract: 

    The Rcs pathway is repressed by the inner membrane protein IgaA under non-stressed conditions. This repression is hypothesized to be relieved by the binding of the outer membrane-anchored RcsF to IgaA. However, the precise mechanism by which RcsF binding triggers the signaling remains unclear. Here, we present the 1.8 Å resolution crystal structure capturing the interaction between IgaA and RcsF. Our comparative structural analysis, examining both the bound and unbound states of the periplasmic domain of IgaA (IgaAp), highlights rotational flexibility within IgaAp. Conversely, the conformation of RcsF remains unchanged upon binding. Our in vivo and in vitro studies do not support the model of a stable complex involving RcsF, IgaAp, and RcsDp. Instead, we demonstrate that the elements beyond IgaAp play a role in the interaction between IgaA and RcsD. These findings collectively allow us to propose a potential mechanism for the signaling across the inner membrane through IgaA.


  • Organizational Affiliation
    • Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA.

Macromolecule Content 

  • Total Structure Weight: 29.88 kDa 
  • Atom Count: 2,148 
  • Modeled Residue Count: 264 
  • Deposited Residue Count: 274 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intracellular growth attenuator protein igaA274Klebsiella pneumoniaeMutation(s): 0 
Gene Names: igaA
UniProt
Find proteins for A0A0H3GWS2 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
Explore A0A0H3GWS2 
Go to UniProtKB:  A0A0H3GWS2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3GWS2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.514α = 90
b = 146.443β = 120.527
c = 52.981γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references
  • Version 1.2: 2024-09-25
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary