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Yorodumi- PDB-6hcg: Klebsiella pneumoniae type II secretion system outer membrane com... -
+Open data
-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. | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Type II secretion system / secretin / outer membrane channel | ||||||
Function / homology | Function and homology information 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 | Klebsiella pneumoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Chernyatina, A.A. / Low, H.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hcg.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hcg.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6hcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/6hcg ftp://data.pdbj.org/pub/pdb/validation_reports/hc/6hcg | HTTPS FTP |
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-Related structure data
Related structure data | 0193MC 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: 70328.633 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: gspD, pulD, B4U30_01620, BANRA_04386, BL124_00006830, C3F39_10150, CK508_015045, E0760_18600, E1814_01470, EAO17_18605, SK89_02022 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J2GHI1, UniProt: A0A0H3GIG3*PLUS #2: Protein | Mass: 15872.848 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BU230_24515 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3GNG8*PLUS #3: Protein | Mass: 30245.924 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) 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: Escherichia coli (E. coli) / References: UniProt: A0A060VDD0, UniProt: A0A0H3GMS7*PLUS |
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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: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO |
Source (natural) | Organism: Klebsiella pneumoniae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Average exposure time: 0.3 sec. / Electron dose: 1.25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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 |