+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19209 | |||||||||
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Title | TadA/CpaF with ADP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pilus / secretion / ATPase / MOTOR PROTEIN | |||||||||
Function / homology | : / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase / Pilus assembly ATPase CpaF Function and homology information | |||||||||
Biological species | Caulobacter vibrioides NA1000 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Hohl M / Low H | |||||||||
Funding support | United Kingdom, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19209.map.gz | 161.7 MB | EMDB map data format | |
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Header (meta data) | emd-19209-v30.xml emd-19209.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_19209.png | 173 KB | ||
Filedesc metadata | emd-19209.cif.gz | 5.6 KB | ||
Others | emd_19209_half_map_1.map.gz emd_19209_half_map_2.map.gz | 139.3 MB 138.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19209 | HTTPS FTP |
-Validation report
Summary document | emd_19209_validation.pdf.gz | 926.7 KB | Display | EMDB validaton report |
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Full document | emd_19209_full_validation.pdf.gz | 926.2 KB | Display | |
Data in XML | emd_19209_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | emd_19209_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19209 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19209 | HTTPS FTP |
-Related structure data
Related structure data | 8rjfMC 8rkdC 8rklC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19209.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19209_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19209_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hexameric complex of TadA bound to ADP
Entire | Name: Hexameric complex of TadA bound to ADP |
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Components |
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-Supramolecule #1: Hexameric complex of TadA bound to ADP
Supramolecule | Name: Hexameric complex of TadA bound to ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
-Macromolecule #1: Pilus assembly ATPase CpaF
Macromolecule | Name: Pilus assembly ATPase CpaF / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
Molecular weight | Theoretical: 46.578355 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: DYYHATKTTI FNALLNTIDL SQLAQLDLKQ AGEEIRDIVA ELVAIKNVSM SVAEQEHLVQ DIINDVLGYG PLEPLLARDD IADIMVNGA HRVFIEVGGK VQLTNVRFRD NLQLMNICQR IVSQVGRRVD ESSPICDARL PDGSRVNVIA PPLALDGPTL T IRKFKKDK ...String: DYYHATKTTI FNALLNTIDL SQLAQLDLKQ AGEEIRDIVA ELVAIKNVSM SVAEQEHLVQ DIINDVLGYG PLEPLLARDD IADIMVNGA HRVFIEVGGK VQLTNVRFRD NLQLMNICQR IVSQVGRRVD ESSPICDARL PDGSRVNVIA PPLALDGPTL T IRKFKKDK LTMKNLVEFA SISPEGARVL GVIGACRCNL VISGGTGSGK TTLLNTMTAF IDPTERVVTC EDAAELQLQQ PH VVRLETR PPNLEGSGAV TMRDLVKNCL RMRPERIIVG EVRGPEAFDL LQAMNTGHDG SMGTLHANSP REAISRIESM ITM GGYGLP SKTIKEMIVG SVDVIIQAAR LRDGSRRITH ITEVVGLEGD VIVTQDLFVY EITGEDEHGK VVGKHRSTGI ARPR FWDRA RYYGLERELA EALDAAEAL UniProtKB: Pilus assembly ATPase CpaF |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Macromolecule | Name: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: EPE |
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Molecular weight | Theoretical: 238.305 Da |
Chemical component information | ChemComp-EPE: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114641 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |