+Open data
-Basic information
Entry | Database: PDB / ID: 8rkd | ||||||
---|---|---|---|---|---|---|---|
Title | TadA/CpaF with AMPPNP | ||||||
Components | Pilus assembly ATPase CpaF | ||||||
Keywords | MOTOR PROTEIN / secretion / ATPase | ||||||
Function / homology | : / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pilus assembly ATPase CpaF Function and homology information | ||||||
Biological species | Caulobacter vibrioides NA1000 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Hohl, M. / Low, H. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2024 Title: Bidirectional pilus processing in the Tad pilus system motor CpaF. Authors: Michael Hohl / Emma J Banks / Max P Manley / Tung B K Le / Harry H Low / Abstract: The bacterial tight adherence pilus system (TadPS) assembles surface pili essential for adhesion and colonisation in many human pathogens. Pilus dynamics are powered by the ATPase CpaF (TadA), which ...The bacterial tight adherence pilus system (TadPS) assembles surface pili essential for adhesion and colonisation in many human pathogens. Pilus dynamics are powered by the ATPase CpaF (TadA), which drives extension and retraction cycles in Caulobacter crescentus through an unknown mechanism. Here we use cryogenic electron microscopy and cell-based light microscopy to characterise CpaF mechanism. We show that CpaF assembles into a hexamer with C2 symmetry in different nucleotide states. Nucleotide cycling occurs through an intra-subunit clamp-like mechanism that promotes sequential conformational changes between subunits. Moreover, a comparison of the active sites with different nucleotides bound suggests a mechanism for bidirectional motion. Conserved CpaF residues, predicted to interact with platform proteins CpaG (TadB) and CpaH (TadC), are mutated in vivo to establish their role in pilus processing. Our findings provide a model for how CpaF drives TadPS pilus dynamics and have broad implications for how other ancient type 4 filament family members power pilus assembly. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8rkd.cif.gz | 747.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8rkd.ent.gz | 626.8 KB | Display | PDB format |
PDBx/mmJSON format | 8rkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rkd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8rkd_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8rkd_validation.xml.gz | 77.5 KB | Display | |
Data in CIF | 8rkd_validation.cif.gz | 111.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/8rkd ftp://data.pdbj.org/pub/pdb/validation_reports/rk/8rkd | HTTPS FTP |
-Related structure data
Related structure data | 19275MC 8rjfC 8rklC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 46465.199 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Gene: cpaF, CCNA_03037 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A0H3CDS2 #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-EPE / #4: Chemical | #5: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hexameric complex of TadA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
Source (recombinant) | Organism: Escherichia coli MC1061 (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21rc1_4933: / Category: model refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73200 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|