7SAX | pdb_00007sax

Structure of GldLM, the proton-powered motor that drives Type IX protein secretion and gliding motility in Sphingobacterium wenxiniae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structures of the Type IX Secretion/Gliding Motility Motor from across the Phylum Bacteroidetes.

Hennell James, R.Deme, J.C.Hunter, A.Berks, B.C.Lea, S.M.

(2022) mBio 13: e0026722-e0026722

  • DOI: https://doi.org/10.1128/mbio.00267-22
  • Primary Citation Related Structures: 
    7SAT, 7SAU, 7SAX, 7SAZ, 7SB2

  • PubMed Abstract: 

    Gliding motility using cell surface adhesins, and export of proteins by the type IX secretion system (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are energized by the GldLM motor complex, which transduces the proton motive force at the inner membrane into mechanical work at the outer membrane. We previously used cryo-electron microscopy to solve the structure of the GldLM motor core from Flavobacterium johnsoniae at 3.9-Å resolution (R. Hennell James, J. C. Deme, A. Kjaer, F. Alcock, et al., Nat Microbiol 6:221-233, 2021, https://dx.doi.org/10.1038/s41564-020-00823-6). Here, we present structures of homologous complexes from a range of pathogenic and environmental Bacteroidetes species at up to 3.0-Å resolution. These structures show that the architecture of the GldLM motor core is conserved across the Bacteroidetes phylum, although there are species-specific differences at the N terminus of GldL. The resolution improvements reveal a cage-like structure that ties together the membrane-proximal cytoplasmic region of GldL and influences gliding function. These findings add detail to our structural understanding of bacterial ion-driven motors that drive the T9SS and gliding motility. IMPORTANCE Many bacteria in the Bacteroidetes phylum use the type IX secretion system to secrete proteins across their outer membrane. Most of these bacteria can also glide across surfaces using adhesin proteins that are propelled across the cell surface. Both secretion and gliding motility are driven by the GldLM protein complex, which forms a nanoscale electrochemical motor. We used cryo-electron microscopy to study the structure of the GldLM protein complex from different species, including the human pathogens Porphyromonas gingivalis and Capnocytophaga canimorsus. The organization of the motor is conserved across species, but we find species-specific structural differences and resolve motor features at higher resolution. This work improves our understanding of the type IX secretion system, which is a virulence determinant in human and animal diseases.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxfordgrid.4991.5, Oxford, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 172.43 kDa 
  • Atom Count: 5,305 
  • Modeled Residue Count: 689 
  • Deposited Residue Count: 1,586 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GldM
A, B
263Sphingobacterium wenxiniaeMutation(s): 0 
Gene Names: SAMN05660206_103134
UniProt
Find proteins for A0A1I6R6I5 (Sphingobacterium wenxiniae)
Explore A0A1I6R6I5 
Go to UniProtKB:  A0A1I6R6I5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I6R6I5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GldL
C, D, E, F, G
212Sphingobacterium wenxiniaeMutation(s): 0 
Gene Names: SAMN05660206_103135
Membrane Entity: Yes 
UniProt
Find proteins for A0A1I6R6J4 (Sphingobacterium wenxiniae)
Explore A0A1I6R6J4 
Go to UniProtKB:  A0A1I6R6J4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I6R6J4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustEuropean Union102164/Z/13/Z
Wellcome TrustEuropean Union107929/Z/15/Z
Wellcome TrustEuropean Union219477/Z/19/Z
European Research Council (ERC)European Union833713

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2022-07-13
    Changes: Database references
  • Version 1.3: 2022-07-20
    Changes: Database references
  • Version 1.4: 2024-06-05
    Changes: Data collection