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Open data
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Basic information
Entry | Database: PDB / ID: 5zdh | ||||||
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Title | CryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex | ||||||
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![]() | PROTEIN TRANSPORT / Pilotin / Secretin | ||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane Similarity search - Function | ||||||
Biological species | Escherichia coli O78:H11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Yin, M. / Yan, Z. / Li, X. | ||||||
![]() | ![]() Title: Structural insight into the assembly of the type II secretion system pilotin-secretin complex from enterotoxigenic Escherichia coli. Authors: Meng Yin / Zhaofeng Yan / Xueming Li / ![]() Abstract: Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II ...Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II secretion system, a lipoprotein called pilotin is essential to bind and target its corresponding secretin to the outer membrane. However, there is only limited structural information available about the interaction and assembly of the pilotin-secretin complex. Here we report the first near-atomic-resolution structure of a full-length Vibrio-type pilotin-secretin (AspS-GspD) complex from enterotoxigenic Escherichia coli by cryo-electron microscopy, which reveals the detailed assembly mode of the full-length pilotin-secretin complex. The AspS subunits attach to the secretin channel surface with a 15:15 stoichiometric ratio to GspD subunits, and insert their amino terminus into the outer membrane. The AspS subunits interact with all three secondary structural elements of the S domain of GspD, including strong interaction with the carboxy-terminal α-helix and weak interactions with another two elements, an α-helix and a loop. These structural and biochemical details provide a deeper insight to pilotin-secretin interaction and their assembly mode. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1022.9 KB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 229.4 KB | Display | |
Data in CIF | ![]() | 350.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6917MC ![]() 6916C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 69700.820 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H10407 / ETEC / Gene: ETEC_3237 / Production host: ![]() ![]() #2: Protein | Mass: 12185.780 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H10407 / ETEC / Gene: ETEC_3239 / Production host: ![]() ![]() |
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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 |
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Sample preparation
Component | Name: Pilotin-Secretin Complex Asps-GspD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: CTFFIND / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37928 / Symmetry type: POINT |