6OKV | pdb_00006okv

PilT4 from Geobacter metallireducens bound to AMP-PNP: C2ccocco conformation

• PDB DOI: https://doi.org/10.2210/pdb6OKV/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Geobacter metallireducens GS-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-15 Released: 2019-11-20 
• Deposition Author(s): McCallum, M., Howell, P.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.01 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

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

• PubMed: 31729381 
• DOI: https://doi.org/10.1038/s41467-019-13070-z
• Primary Citation Related Structures: 
  6OJX, 6OJY, 6OJZ, 6OK2, 6OKV, 6OLJ, 6OLK, 6OLL, 6OLM


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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. [e-mail].
Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. [e-mail].
Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1l7, Canada. [e-mail].
Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada. [e-mail].
Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. [e-mail].
Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 260.28 kDa 
• Atom Count: 16,189 
• Modeled Residue Count: 2,117 
• Deposited Residue Count: 2,310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twitching motility pilus retraction ATPase	A, B, C, D, E, F	385	Geobacter metallireducens GS-15	Mutation(s): 0  Gene Names: pilT-4, Gmet_1394
UniProt
Find proteins for Q39VU6 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39VU6  Go to UniProtKB:  Q39VU6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	H [auth A], J [auth B], M [auth D], O [auth E]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADP	K [auth C], P [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	G [auth A], I [auth B], L [auth D], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.01 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.51	α = 90
b = 127.13	β = 90
c = 187.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): McCallum, M., Howell, P.L.

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Funding Organization	Location	Grant 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
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description