3LW9 | pdb_00003lw9

Structure of a Cytoplasmic Domain of Salmonella InvA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.238 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

A conserved domain in type III secretion links the cytoplasmic domain of InvA to elements of the basal body.

Lilic, M., Quezada, C.M., Stebbins, C.E.

(2010) Acta Crystallogr D Biol Crystallogr 66: 709-713

  • DOI: https://doi.org/10.1107/S0907444910010796
  • Primary Citation Related Structures: 
    3LW9

  • PubMed Abstract: 

    Protein type III secretion systems (T3SSs) are organic nanosyringes that achieve an energy-dependent translocation of bacterial proteins through the two membranes of Gram-negative organisms. Examples include the pathogenic systems of animals, plants and symbiotic bacteria that inject factors into eukaryotic cells, and the flagellar export system that secretes flagellin. T3SSs possess a core of several membrane-associated proteins that are conserved across all known bacterial species that use this system. The Salmonella protein InvA is one of the most highly conserved proteins of this core of critical T3SS components. The crystal structure of a C-terminal domain of InvA reveals an unexpected homology to domains that have been repeatedly found as building blocks of other elements of the T3SS apparatus. This suggests the surprising hypothesis that evolution has produced a significant component of the apparatus structure through a series of gene-duplication and gene-rearrangement events.

    • Organizational Affiliation: 
    • Laboratory of Structural Microbiology, The Rockefeller University, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 39.68 kDa 
  • Atom Count: 2,916 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Invasion protein invA
A, B
168Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 2 
Gene Names: invA, STM2896
UniProt
Find proteins for P0A1I3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1I3 
Go to UniProtKB:  P0A1I3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1I3
Sequence Annotations
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Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.238 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.682α = 90
b = 83.682β = 90
c = 130.389γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXphasing
PHENIXphasing
ARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-20
    Changes: Data collection, Structure summary