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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3882 | |||||||||
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Title | Thermus thermophilus PilF ATPase (apoprotein form) | |||||||||
![]() | Thermus thermophilus PilF ATPase (apoprotein form) | |||||||||
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Function / homology | ![]() ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Derrick JP / Collins RF | |||||||||
![]() | ![]() Title: Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly. Authors: Richard Collins / Vijaykumar Karuppiah / C Alistair Siebert / Rana Dajani / Angela Thistlethwaite / Jeremy P Derrick / ![]() Abstract: Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an ...Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an inner membrane complex of biogenesis proteins which, in turn, bind to nascent pilin subunits and mediate fiber assembly. Here we report the structural characterization of the PilF TFP assembly ATPase from Thermus thermophilus. The crystal structure of a recombinant C-terminal fragment of PilF revealed bound, unhydrolysed ATP, although the full length complex was enzymatically active. 3D reconstructions were carried out by single particle cryoelectron microscopy for full length apoprotein PilF and in complex with AMPPNP. The structure forms an hourglass-like shape, with the ATPase domains in one half and the N1 domains in the second half which, we propose, interact with the other pilus biogenesis components. Molecular models for both forms were generated: binding of AMPPNP causes an upward shift of the N1 domains towards the ATPase domains of ~8 Å. We advocate a model in which ATP hydrolysis is linked to displacement of the N1 domains which is associated with lifting pilin subunits out of the inner membrane, and provide the activation energy needed to form the pilus fiber. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 72.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 220.9 KB | Display | ![]() |
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Full document | ![]() | 220.1 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ejfMC ![]() 4194C ![]() 5oiuC ![]() 6f8lC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Thermus thermophilus PilF ATPase (apoprotein form) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Thermus thermophilus PilF ATPase (AMPPNP-bound form)
Entire | Name: Thermus thermophilus PilF ATPase (AMPPNP-bound form) |
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Components |
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-Supramolecule #1: Thermus thermophilus PilF ATPase (AMPPNP-bound form)
Supramolecule | Name: Thermus thermophilus PilF ATPase (AMPPNP-bound form) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Type IV pilus assembly protein PilF
Macromolecule | Name: Type IV pilus assembly protein PilF / type: protein_or_peptide / ID: 1 Details: Domain is part of the larger protein but connectivity to other domains cannot be confirmed. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 |
Molecular weight | Theoretical: 16.249751 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LPRAKPLGEI LVELGLARPE DVEEALQKQR RGGGRLEDTL VQSGKLRPEA LAQAVATQLG YPYVDPEEDP PDPGAPLLLP EDLCRRYGV FPHRLEGNRL VLLMKDPRNI LALDDVRLAL KRKGLNYEVA PAVATEAAIT KLIERFY |
-Macromolecule #2: Type IV pilus assembly protein PilF
Macromolecule | Name: Type IV pilus assembly protein PilF / type: protein_or_peptide / ID: 2 Details: Domain is part of the larger protein but connectivity to other domains cannot be confirmed. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 |
Molecular weight | Theoretical: 15.440708 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QKDLKLGELL LQKGWISREA LEEALVEQEK TGDLLGRILV RKGLPEEALY RALAEQKGLE FLESTEGIVP DPSAALLLLR SDALRYGAV PIGFQNGEVE VVLSDPRHKE AVAQLLNRPA RFYLALPQAW EELFRRAY |
-Macromolecule #3: Type IV pilus assembly protein PilF
Macromolecule | Name: Type IV pilus assembly protein PilF / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 |
Molecular weight | Theoretical: 45.203906 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SAAQKFVKQV IREAFLQDAS DIHIEPRQND VQVRLRIDGA LRPYSTLPKG ALNAVISVVK IMGGLNIAEK RLPQDGRVRY REGAIDVDL RLSTLPTVYG EKAVMRLLKK ASDIPEIEDL GFAPGVFERF KEVISKPYGI FLITGPTGSG KSFTTFSILK R IATPDKNT ...String: SAAQKFVKQV IREAFLQDAS DIHIEPRQND VQVRLRIDGA LRPYSTLPKG ALNAVISVVK IMGGLNIAEK RLPQDGRVRY REGAIDVDL RLSTLPTVYG EKAVMRLLKK ASDIPEIEDL GFAPGVFERF KEVISKPYGI FLITGPTGSG KSFTTFSILK R IATPDKNT QTIEDPVEYE IPGINQTQVN PQAGLTFARA LRAFLRQDPD IIMVGEIRDS ETAKIATEAA LTGHLVIATL HT NDAAQAI TRLDEMGVEP FNISAALIGV LSQRLVRRVC EHCKVEVKPD PETLRRLGLS EAEIQGARLY KGMGCERCGG TGY KGRYAI HELLVVDDEI RHAIVAGKSA TEIKEIARRK GMKTLREDGL YKALQGITTL EEVLARTIEA AAELALVPRG SSAH HHHHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 Details: 25 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2 and 5 % glycerol (v/v) |
Vitrification | Cryogen name: ETHANE |
Details | Monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 45000 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6ejf: |