9E29 | pdb_00009e29

Expanded structure of CpaF with two ATPs and four ADPs (Saturated ATP dataset)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly.

Yen, I.Y.Whitfield, G.B.Rubinstein, J.L.Burrows, L.L.Brun, Y.V.Howell, P.L.

(2025) Nat Commun 16: 3839-3839

  • DOI: https://doi.org/10.1038/s41467-025-59009-5
  • Primary Citation of Related Structures:  
    9E24, 9E25, 9E26, 9E27, 9E29

  • PubMed Abstract: 

    The type IV pilus family uses PilT/VirB11-like ATPases to rapidly assemble and disassemble pilin subunits. Among these, the tight adherence (Tad) pilus performs both functions using a single bifunctional ATPase, CpaF. Here, we determine three conformationally distinct structures of CpaF hexamers with varying nucleotide occupancies by cryo-electron microscopy. Analysis of these structures suggest ATP binding and hydrolysis expand and rotate the hexamer pore clockwise while subsequent ADP release contracts the ATPase. Truncation of the intrinsically disordered region of CpaF in Caulobacter crescentus equally reduces pilus extension and retraction events observed using fluorescence microscopy, but does not reduce ATPase activity. AlphaFold3 modeling suggests that CpaF and other motors of the type IV filament superfamily employ conserved secondary structural features to engage their respective platform proteins. From these data, we propose that CpaF uses a clockwise, rotary mechanism of catalysis to assemble a right-handed, helical Tad pilus, a process broadly applicable to other single motor systems.


  • Organizational Affiliation
    • Program in Molecular Medicine, Peter Gilgan Center for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CpaF
A, B, C, D, E
A, B, C, D, E, F
501Caulobacter vibrioides NA1000Mutation(s): 0 
Gene Names: cpaF
UniProt
Find proteins for Q9L714 (Caulobacter vibrioides)
Explore Q9L714 
Go to UniProtKB:  Q9L714
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L714
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
N [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
J [auth B],
L [auth C],
O [auth E],
Q [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
P [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
P [auth E],
R [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-169053

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references