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Yorodumi- PDB-6olj: CryoEM structure of PilB from Geobacter metallireducens: C2ccocco... -
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-Basic information
Entry | Database: PDB / ID: 6olj | ||||||
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Title | CryoEM structure of PilB from Geobacter metallireducens: C2ccocco conformation | ||||||
Components | Type IV pilus biogenesis ATPase PilB | ||||||
Keywords | MOTOR PROTEIN / ATPase / T4P / type iv pilus / motor | ||||||
Function / homology | Function and homology information pilus assembly / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacter metallireducens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
Authors | McCallum, M. / Howell, P.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Multiple conformations facilitate PilT function in the type IV pilus. Authors: Matthew McCallum / Samir Benlekbir / Sheryl Nguyen / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell / 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 ...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 symmetry; however, most of these ATPases crystallize with either C or C 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 C, and C 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 conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6olj.cif.gz | 422 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6olj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6olj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6olj_validation.pdf.gz | 920.6 KB | Display | wwPDB validaton report |
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Full document | 6olj_full_validation.pdf.gz | 923.3 KB | Display | |
Data in XML | 6olj_validation.xml.gz | 55 KB | Display | |
Data in CIF | 6olj_validation.cif.gz | 89.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/6olj ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6olj | HTTPS FTP |
-Related structure data
Related structure data | 20114MC 6ojxC 6ojyC 6ojzC 6ok2C 6okvC 6olkC 6ollC 6olmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 64899.281 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilB, Gmet_1393 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU7 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PilB Hexamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Geobacter metallireducens (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pET28a |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Homemade |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3257 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 68.8 / Protocol: FLEXIBLE FIT Details: Initial fitting in chimera, flexible fitting in Phenix-refine | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5TSG |