6OK2

PilT4 from Geobacter metallireducens bound to ADP: C3ocococ conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.287 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Multiple conformations facilitate PilT function in the type IV pilus.

McCallum, M.Benlekbir, S.Nguyen, S.Tammam, S.Rubinstein, J.L.Burrows, L.L.Howell, P.L.

(2019) Nat Commun 10: 5198-5198

  • DOI: 10.1038/s41467-019-13070-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This fa ...

    Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C 2 symmetry; however, most of these ATPases crystallize with either C 3 or C 6 symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C 2, C 3 , and C 6 conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C 2 conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members.


    Organizational Affiliation

    Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. john.rubinstein@utoronto.ca.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1l7, Canada. john.rubinstein@utoronto.ca.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada. burrowl@mcmaster.ca.,Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. howell@sickkids.ca.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. howell@sickkids.ca.,Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. john.rubinstein@utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
A, B, C, D, E, F
385Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)Mutation(s): 0 
Gene Names: pilT-4
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.287 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 111.817α = 90.00
b = 120.956β = 90.00
c = 185.915γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references
  • Version 1.2: 2020-01-08
    Type: Author supporting evidence