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- PDB-6hcg: Klebsiella pneumoniae type II secretion system outer membrane com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hcg | ||||||
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Title | Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain. | ||||||
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![]() | PROTEIN TRANSPORT / Type II secretion system / secretin / outer membrane channel | ||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / intracellular protein transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
![]() | Chernyatina, A.A. / Low, H.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Core architecture of a bacterial type II secretion system. Authors: Anastasia A Chernyatina / Harry H Low / ![]() Abstract: Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the ...Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae. We show that 7 proteins form a ~2.4 MDa complex that spans the cell envelope. The outer membrane complex includes the secretin PulD, with all domains modelled, and the pilotin PulS. The inner membrane assembly platform components PulC, PulE, PulL, PulM and PulN have a relative stoichiometric ratio of 2:1:1:1:1. The PulE ATPase, PulL and PulM combine to form a flexible hexameric hub. Symmetry mismatch between the outer membrane complex and assembly platform is overcome by PulC linkers spanning the periplasm, with PulC HR domains binding independently at the secretin base. Our results show that the T2SS has a highly dynamic modular architecture, with implication for pseudo-pilus assembly and substrate loading. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 239 KB | Display | |
Data in CIF | ![]() | 385.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0193MC 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: 70328.633 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gspD, pulD, B4U30_01620, BANRA_04386, BL124_00006830, C3F39_10150, CK508_015045, E0760_18600, E1814_01470, EAO17_18605, SK89_02022 Production host: ![]() ![]() #2: Protein | Mass: 15872.848 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 30245.924 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pulC, gspC, outC, B1727_29100, B4U22_01185, BL124_0006760, C3F39_10145, C9J88_23460, CPT10_02240, CSC88_13925, CWQ24_23120, KpST82_0728, PMK1_02469, SM57_00150 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: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain. Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
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 | Average exposure time: 0.3 sec. / Electron dose: 1.25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C15 (15 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7284 / Symmetry type: POINT |