4O3V

Crystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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This is version 1.3 of the entry. See complete history


Literature

Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems.

Gillespie, J.J.Phan, I.Q.Scheib, H.Subramanian, S.Edwards, T.E.Lehman, S.S.Piitulainen, H.Rahman, M.S.Rennoll-Bankert, K.E.Staker, B.L.Taira, S.Stacy, R.Myler, P.J.Azad, A.F.Pulliainen, A.T.

(2015) mBio 6: e01867-e01815

  • DOI: 10.1128/mBio.01867-15
  • Primary Citation of Related Structures:  
    4JF8, 4KZ1, 4LSO, 4MEI, 4NHF, 4O3V

  • PubMed Abstract: 
  • Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw) ...

    Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw). In a unique case, most rickettsial species encode a T4SS (rvh) enriched with gene duplication. Within single genomes, the evolutionary and functional implications of cross-system interchangeability of analogous T4SS protein components remains poorly understood. To lend insight into cross-system interchangeability, we analyzed the VirB8 family of T4SS channel proteins. Crystal structures of three VirB8 and two TrwG Bartonella proteins revealed highly conserved C-terminal periplasmic domain folds and dimerization interfaces, despite tremendous sequence divergence. This implies remarkable structural constraints for VirB8 components in the assembly of a functional T4SS. VirB8/TrwG heterodimers, determined via bacterial two-hybrid assays and molecular modeling, indicate that differential expression of trw and vir systems is the likely barrier to VirB8-TrwG interchangeability. We also determined the crystal structure of Rickettsia typhi RvhB8-II and modeled its coexpressed divergent paralog RvhB8-I. Remarkably, while RvhB8-I dimerizes and is structurally similar to other VirB8 proteins, the RvhB8-II dimer interface deviates substantially from other VirB8 structures, potentially preventing RvhB8-I/RvhB8-II heterodimerization. For the rvh T4SS, the evolution of divergent VirB8 paralogs implies a functional diversification that is unknown in other T4SSs. Collectively, our data identify two different constraints (spatiotemporal for Bartonella trw and vir T4SSs and structural for rvh T4SSs) that mediate the functionality of multiple divergent T4SSs within a single bacterium.


    Related Citations: 
    • The Rickettsia type IV secretion system: unrealized complexity mired by gene family expansion.
      Gillespie, J.J., Phan, I.Q., Driscoll, T.P., Guillotte, M.L., Lehman, S.S., Rennoll-Bankert, K.E., Subramanian, S., Beier-Sexton, M., Myler, P.J., Rahman, M.S., Azad, A.F.
      (2016) Pathog Dis --: --

    Organizational Affiliation

    Department of Biosciences, University of Helsinki, Helsinki, Finland Institute of Biomedicine, University of Turku, Turku, Finland JGillespie@som.umaryland.edu arto.pulliainen@utu.fi.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VirB8-like protein of type IV secretion systemA, B181Rickettsia typhi str. WilmingtonMutation(s): 0 
Gene Names: RT0278
UniProt
Find proteins for Q68X84 (Rickettsia typhi (strain ATCC VR-144 / Wilmington))
Explore Q68X84 
Go to UniProtKB:  Q68X84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68X84
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRT
Query on SRT

Download Ideal Coordinates CCD File 
C [auth B]S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.18430/M34O3V
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.68α = 90
b = 117.68β = 90
c = 83.82γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2016-06-29
    Changes: Database references