Crystal Structure of ATPase delta1-79 Spa47 R271A

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

Currently 6N73 does not have a validation slider image.

This is version 1.4 of the entry. See complete history


Interfacial amino acids support Spa47 oligomerization and shigella type three secretion system activation.

Demler, H.J.Case, H.B.Morales, Y.Bernard, A.R.Johnson, S.J.Dickenson, N.E.

(2019) Proteins 87: 931-942

  • DOI: https://doi.org/10.1002/prot.25754
  • Primary Citation of Related Structures:  
    6N6L, 6N6M, 6N6Z, 6N70, 6N71, 6N72, 6N73, 6N74, 6N75, 6N76

  • PubMed Abstract: 

    Like many Gram-negative pathogens, Shigella rely on a type three secretion system (T3SS) for injection of effector proteins directly into eukaryotic host cells to initiate and sustain infection. Protein secretion through the needle-like type three secretion apparatus (T3SA) requires ATP hydrolysis by the T3SS ATPase Spa47, making it a likely target for in vivo regulation of T3SS activity and an attractive target for small molecule therapeutics against shigellosis. Here, we developed a model of an activated Spa47 homo-hexamer, identifying two distinct regions at each protomer interface that we hypothesized to provide intermolecular interactions supporting Spa47 oligomerization and enzymatic activation. Mutational analysis and a series of high-resolution crystal structures confirm the importance of these residues, as many of the engineered mutants are unable to form oligomers and efficiently hydrolyze ATP in vitro. Furthermore, in vivo evaluation of Shigella virulence phenotype uncovered a strong correlation between T3SS effector protein secretion, host cell membrane disruption, and cellular invasion by the tested mutant strains, suggesting that perturbation of the identified interfacial residues/interactions influences Spa47 activity through preventing oligomer formation, which in turn regulates Shigella virulence. The most impactful mutations are observed within the conserved Site 2 interface where the native residues support oligomerization and likely contribute to a complex hydrogen bonding network that organizes the active site and supports catalysis. The critical reliance on these conserved residues suggests that aspects of T3SS regulation may also be conserved, providing promise for the development of a cross-species therapeutic that broadly targets T3SS ATPase oligomerization and activation.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, Utah.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase SpaL/MxiB
A, B
352Shigella flexneriMutation(s): 1 
Gene Names: spaLmxiBspa47CP0149sctN
EC: (PDB Primary Data), (UniProt)
Find proteins for P0A1C1 (Shigella flexneri)
Explore P0A1C1 
Go to UniProtKB:  P0A1C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1C1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.199α = 90
b = 154.117β = 110.03
c = 54.905γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Currently 6N73 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R15AI124108-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description