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- PDB-6hcg: Klebsiella pneumoniae type II secretion system outer membrane com... -

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Basic information

Entry
Database: PDB / ID: 6hcg
TitleKlebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.
Components
  • Pectic enzymes secretion protein OutC
  • Pullulanase
  • Type II secretion system protein DType II secretion system
KeywordsPROTEIN 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 / intracellular protein transport / cell outer membrane / integral component of membrane / plasma membrane
Type II secretion system protein C / Chaperone lipoprotein, PulS/OutS / Type II secretion system pilotin lipoprotein (PulS_OutS) / Bacterial type II/III secretion system short domain / Bacterial type II and III secretion system protein / NolW-like superfamily / PulS/OutS-like superfamily / PDZ superfamily / Type II secretion system protein GspC, N-terminal / Type II secretion system protein GspD ...Type II secretion system protein C / Chaperone lipoprotein, PulS/OutS / Type II secretion system pilotin lipoprotein (PulS_OutS) / Bacterial type II/III secretion system short domain / Bacterial type II and III secretion system protein / NolW-like superfamily / PulS/OutS-like superfamily / PDZ superfamily / Type II secretion system protein GspC, N-terminal / Type II secretion system protein GspD / Chaperone lipoprotein, PulS/OutS-like / NolW-like / Type II/III secretion system / Type II secretion system protein GspD, conserved site / GspD/PilQ family / Type II secretion system protein GspC
General secretion pathway protein C / Pullulanase D protein / Pullulanase-specific type II secretion system component C / Pullulanase secretion protein PulS / General secretion pathway protein D
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsChernyatina, A.A. / Low, H.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200074/Z/15/Z United Kingdom
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Type II secretion system protein D
B: Type II secretion system protein D
C: Type II secretion system protein D
D: Type II secretion system protein D
E: Type II secretion system protein D
F: Type II secretion system protein D
G: Type II secretion system protein D
H: Type II secretion system protein D
I: Type II secretion system protein D
J: Type II secretion system protein D
K: Type II secretion system protein D
L: Type II secretion system protein D
M: Type II secretion system protein D
N: Type II secretion system protein D
O: Type II secretion system protein D
P: Pullulanase
Q: Pullulanase
R: Pullulanase
S: Pullulanase
T: Pullulanase
U: Pullulanase
V: Pullulanase
W: Pullulanase
X: Pullulanase
Y: Pullulanase
Z: Pullulanase
a: Pullulanase
b: Pullulanase
c: Pullulanase
d: Pullulanase
e: Pectic enzymes secretion protein OutC
f: Pectic enzymes secretion protein OutC
g: Pectic enzymes secretion protein OutC
h: Pectic enzymes secretion protein OutC
i: Pectic enzymes secretion protein OutC
j: Pectic enzymes secretion protein OutC
k: Pectic enzymes secretion protein OutC
l: Pectic enzymes secretion protein OutC
m: Pectic enzymes secretion protein OutC
n: Pectic enzymes secretion protein OutC
o: Pectic enzymes secretion protein OutC
p: Pectic enzymes secretion protein OutC
q: Pectic enzymes secretion protein OutC
r: Pectic enzymes secretion protein OutC
s: Pectic enzymes secretion protein OutC


Theoretical massNumber of molelcules
Total (without water)1,746,71145
Polymers1,746,71145
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Type II secretion system protein D / Type II secretion system / Type II secretion system protein GspD


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
Pullulanase /


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
Pectic enzymes secretion protein OutC / PulC protein / Type II secretion system protein C / Type II secretion system protein GspC


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage 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
IDNameVersionCategory
4Gctf1.06CTF correction
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7284 / Symmetry type: POINT

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