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Yorodumi- PDB-6ysl: Structure of the flagellar MotAB stator complex from Bacillus subtilis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ysl | |||||||||||||||
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Title | Structure of the flagellar MotAB stator complex from Bacillus subtilis | |||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Stator Flagellar rotation ion driven motor | |||||||||||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum-dependent swarming motility / monoatomic ion transport / chemotaxis / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Lea, S.M. / Deme, J.C. / Johnson, S.J. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structures of the stator complex that drives rotation of the bacterial flagellum. Authors: Justin C Deme / Steven Johnson / Owen Vickery / Amy Aron / Holly Monkhouse / Thomas Griffiths / Rory Hennell James / Ben C Berks / James W Coulton / Phillip J Stansfeld / Susan M Lea / Abstract: The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor ...The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio mimicus, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric AB subunit assembly where the five A subunits enclose the two B subunits. Comparison to structures of other ion-driven motors indicates that this AB architecture is fundamental to bacterial systems that couple energy from ion flow to generate mechanical work at a distance and suggests that such events involve rotation in the motor structures. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ysl.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ysl.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ysl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ysl_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6ysl_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ysl_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 6ysl_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/6ysl ftp://data.pdbj.org/pub/pdb/validation_reports/ys/6ysl | HTTPS FTP |
-Related structure data
Related structure data | 10899MC 6ysfC 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: 29370.221 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: motA, BSU13690 / Production host: Escherichia coli (E. coli) / References: UniProt: P28611 #2: Protein | Mass: 29529.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: motB, BSU13680 / Production host: Escherichia coli (E. coli) / References: UniProt: P28612 |
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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: MotA(5)B(2) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
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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 |
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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 magnification: 165000 X / Nominal defocus max: 0.3 nm / Nominal defocus min: 0.1 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3126: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1532430 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122615 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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