+Open data
-Basic information
Entry | Database: PDB / ID: 8bri | ||||||||||||
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Title | VaPomAB MSP1D1 nanodisc | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Flagellar sodium-driven stator unit | ||||||||||||
Function / homology | Function and homology information bacterial-type flagellum-dependent swarming motility / proton transmembrane transport / chemotaxis / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Vibrio alginolyticus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Hu, H. / Taylor, N.M.I. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit. Authors: Haidai Hu / Philipp F Popp / Mònica Santiveri / Aritz Roa-Eguiara / Yumeng Yan / Freddie J O Martin / Zheyi Liu / Navish Wadhwa / Yong Wang / Marc Erhardt / Nicholas M I Taylor / Abstract: Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively ...Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bri.cif.gz | 228.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bri.ent.gz | 183.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bri_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8bri_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8bri_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 8bri_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/8bri ftp://data.pdbj.org/pub/pdb/validation_reports/br/8bri | HTTPS FTP |
-Related structure data
Related structure data | 16215MC 8brdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 27283.031 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: pomA / Production host: Escherichia coli (E. coli) / References: UniProt: O06873 #2: Protein | Mass: 35587.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: N646_2843 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I3CFY6 |
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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: flagellar sodium-driven stator unit / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: 300mM NaCl, 20mM HEPES 7.5, 0.002%LMNG |
Specimen | Conc.: 16 mg/ml / 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||
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CTF correction | Type: NONE | ||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Num. of particles: 66296 / Symmetry type: POINT | ||||||||||||
Refine LS restraints |
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