6OJY

Methylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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
  • Structures With Same Primary Citation

  • 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. howell@sickkids.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
A
385Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: pilT-4Gmet_1394
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
B
385Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: pilT-4Gmet_1394
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
C
385Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: pilT-4Gmet_1394
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
D, E
385Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: pilT-4Gmet_1394
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Twitching motility pilus retraction ATPase
F
385Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: pilT-4Gmet_1394
Find proteins for Q39VU6 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39VU6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.8α = 90
b = 119.01β = 90
c = 178.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence