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Yorodumi- PDB-7amy: Nonameric cytoplasmic domain of FlhA from Vibrio parahaemolyticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 7amy | ||||||||||||||||||
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Title | Nonameric cytoplasmic domain of FlhA from Vibrio parahaemolyticus | ||||||||||||||||||
Components | Flagellar biosynthesis protein FlhA | ||||||||||||||||||
Keywords | PROTEIN TRANSPORT / T3SS / export apparatus / secretion / protein export / motility | ||||||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å | ||||||||||||||||||
Authors | Kuhlen, L. / Johnson, S. / Lea, S. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: PLoS One / Year: 2021 Title: Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein. Authors: Lucas Kuhlen / Steven Johnson / Jerry Cao / Justin C Deme / Susan M Lea / Abstract: Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which ...Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomer's cytoplasmic domain, which stabilises the nonameric ring assembly. | ||||||||||||||||||
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 | 7amy.cif.gz | 567.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7amy.ent.gz | 455.8 KB | Display | PDB format |
PDBx/mmJSON format | 7amy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7amy_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7amy_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7amy_validation.xml.gz | 107.7 KB | Display | |
Data in CIF | 7amy_validation.cif.gz | 146.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/7amy ftp://data.pdbj.org/pub/pdb/validation_reports/am/7amy | HTTPS FTP |
-Related structure data
Related structure data | 11827MC 7alwC 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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-Components
#1: Protein | Mass: 76555.820 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) Gene: flhA, C1S91_05000, C9I78_24000, CGI34_13080, D5E78_16030, E4P16_05430, F0L99_07770, WR32_16185 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F5SXE4 |
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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: Nonamer of the FlhA cytoplasmic domain from Vibrio parahaemolyticus Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.7 MDa / Experimental value: NO |
Source (natural) | Organism: Vibrio parahaemolyticus (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18rc1_3769: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C9 (9 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9756 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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