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- PDB-6q14: Structure of the Salmonella SPI-1 injectisome NC-base -

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Basic information

Entry
Database: PDB / ID: 6q14
TitleStructure of the Salmonella SPI-1 injectisome NC-base
Components
  • (Surface presentation of antigens protein ...) x 3
  • Lipoprotein PrgK
  • Protein InvG
  • Protein PrgH
KeywordsPROTEIN TRANSPORT / Bacterial secretion / type III secretion
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / cell outer membrane / identical protein binding / plasma membrane
Similarity search - Function
Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. ...Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / Type III secretion system, PrgH/EprH-like / FliP family / Type III secretion system protein PrgH-EprH (PrgH) / Flagella transport protein fliP family signature 2. / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Surface presentation of antigens protein SpaQ / SPI-1 type 3 secretion system secretin / Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaR / Protein PrgH / Lipoprotein PrgK
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHu, J. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Microbiol / Year: 2019
Title: T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly.
Authors: Jinhong Hu / Liam J Worrall / Marija Vuckovic / Chuan Hong / Wanyin Deng / Claire E Atkinson / B Brett Finlay / Zhiheng Yu / Natalie C J Strynadka /
Abstract: The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, ...The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. Bacterial proteins destined for self-assembly and host-cell targeting are translocated by the injectisome in a process known as type III secretion (T3S). The core structure is the ~4 MDa needle complex (NC), built on a foundation of three highly oligomerized ring-forming proteins that create a hollow scaffold spanning the bacterial inner membrane (IM) (24-mer ring-forming proteins PrgH and PrgK in the Salmonella enterica serovar Typhimurium Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS)) and outer membrane (OM) (15-mer InvG, a member of the broadly conserved secretin pore family). An internalized helical needle projects from the NC and bacterium, ultimately forming a continuous passage to the host, for delivery of virulence effectors. Here, we have captured snapshots of the entire prototypical SPI-1 NC in four distinct needle assembly states, including near-atomic resolution, and local reconstructions in the absence and presence of the needle. These structures reveal the precise localization and molecular interactions of the internalized SpaPQR 'export apparatus' complex, which is intimately encapsulated and stabilized within the IM rings in the manner of a nanodisc, and to which the PrgJ rod directly binds and functions as an initiator and anchor of needle polymerization. We also describe the molecular details of the extensive and continuous coupling interface between the OM secretin and IM rings, which is remarkably facilitated by a localized 16-mer stoichiometry in the periplasmic-most coupling domain of the otherwise 15-mer InvG oligomer.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
AA: Lipoprotein PrgK
AB: Lipoprotein PrgK
AC: Lipoprotein PrgK
AD: Lipoprotein PrgK
AE: Lipoprotein PrgK
AF: Lipoprotein PrgK
AG: Lipoprotein PrgK
0: Surface presentation of antigens protein SpaP
1: Surface presentation of antigens protein SpaP
2: Surface presentation of antigens protein SpaP
3: Surface presentation of antigens protein SpaP
4: Surface presentation of antigens protein SpaP
5: Surface presentation of antigens protein SpaR
6: Surface presentation of antigens protein SpaQ
7: Surface presentation of antigens protein SpaQ
8: Surface presentation of antigens protein SpaQ
9: Surface presentation of antigens protein SpaQ
AH: Lipoprotein PrgK
AI: Lipoprotein PrgK
E: Protein PrgH
Q: Protein InvG
R: Protein PrgH
S: Protein PrgH
T: Protein PrgH
U: Protein PrgH
V: Protein PrgH
W: Protein PrgH
X: Protein PrgH
Y: Protein PrgH
Z: Protein PrgH
AL: Lipoprotein PrgK
a: Protein PrgH
b: Protein PrgH
c: Protein PrgH
d: Protein PrgH
e: Protein PrgH
f: Protein PrgH
g: Protein PrgH
h: Protein PrgH
i: Protein PrgH
j: Protein PrgH
k: Protein PrgH
l: Protein PrgH
m: Protein PrgH
n: Protein PrgH
o: Lipoprotein PrgK
p: Lipoprotein PrgK
q: Lipoprotein PrgK
r: Lipoprotein PrgK
s: Lipoprotein PrgK
t: Lipoprotein PrgK
u: Lipoprotein PrgK
v: Lipoprotein PrgK
w: Lipoprotein PrgK
x: Lipoprotein PrgK
y: Lipoprotein PrgK
z: Lipoprotein PrgK
AJ: Lipoprotein PrgK
AK: Lipoprotein PrgK
A: Protein InvG
B: Protein InvG
C: Protein InvG
D: Protein InvG
F: Protein InvG
G: Protein InvG
H: Protein InvG
I: Protein InvG
J: Protein InvG
K: Protein InvG
L: Protein InvG
M: Protein InvG
N: Protein InvG
O: Protein InvG
P: Protein InvG


Theoretical massNumber of molelcules
Total (without water)2,927,68174
Polymers2,927,68174
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area536340 Å2
ΔGint-2415 kcal/mol
Surface area747050 Å2

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Components

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Protein , 3 types, 64 molecules AAABACADAEAFAGAHAIALopqrstuvwxyzAJAKERSTUV...

#1: Protein ...
Lipoprotein PrgK


Mass: 28245.287 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P41786
#5: Protein ...
Protein PrgH


Mass: 44509.367 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P41783
#6: Protein
Protein InvG


Mass: 61835.559 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P35672

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Surface presentation of antigens protein ... , 3 types, 10 molecules 0123456789

#2: Protein
Surface presentation of antigens protein SpaP


Mass: 25249.596 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P40700
#3: Protein Surface presentation of antigens protein SpaR


Mass: 28499.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P40701
#4: Protein
Surface presentation of antigens protein SpaQ


Mass: 9363.229 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1L7

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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: SPI-1 injectisome NC-base / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 3 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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 recordingElectron dose: 51.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51816 / Symmetry type: POINT

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