+Open data
-Basic information
Entry | Database: PDB / ID: 7clr | |||||||||
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Title | CryoEM structure of S.typhimurium flagellar LP ring | |||||||||
Components |
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Keywords | MOTOR PROTEIN / FlgH / FlgI / LP ring / Bushing / Salmonella / Flagellar motor | |||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Yamaguchi, T. / Makino, F. / Miyata, T. / Minamino, T. / Kato, T. / Namba, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of the molecular bushing of the bacterial flagellar motor. Authors: Tomoko Yamaguchi / Fumiaki Makino / Tomoko Miyata / Tohru Minamino / Takayuki Kato / Keiichi Namba / Abstract: The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable ...The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface. | |||||||||
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 | 7clr.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7clr.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 7clr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/7clr ftp://data.pdbj.org/pub/pdb/validation_reports/cl/7clr | HTTPS FTP |
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-Related structure data
Related structure data | 30398MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 38194.176 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Details: SJW2177 / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: A0A0F7J5J5 #2: Protein | Mass: 24726.666 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Details: SJW2177 / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: A0A0J5DWE9 |
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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: LP ring / Type: COMPLEX / Details: Bushing of flagellar motor / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: HK1002 | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
EM embedding | Material: buffer | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 200 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 275 nm / Calibrated defocus max: 8230 nm / Cs: 1.4 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 12759 |
EM imaging optics | Energyfilter name: In-column Omega Filter |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 64418 Details: particles were picked up by YOLOPick.py (in-house python program) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C26 (26 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10802 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 38 / Protocol: OTHER / Space: REAL |