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- PDB-6pep: Focussed refinement of InvGN0N1:SpaPQR:PrgIJ from the Salmonella ... -

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Entry
Database: PDB / ID: 6pep
TitleFocussed refinement of InvGN0N1:SpaPQR:PrgIJ from the Salmonella SPI-1 injectisome needle complex
Components
  • (Surface presentation of antigens protein ...) x 3
  • Protein InvG
  • Protein PrgH
  • Protein PrgI
  • Protein PrgJ
KeywordsPROTEIN TRANSPORT / Bacterial secretion / type III secretion
Function / homology
Function and homology information


The IPAF inflammasome / type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / cell outer membrane / protein transport ...The IPAF inflammasome / type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / cell outer membrane / protein transport / cell surface / extracellular region / 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, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC ...: / 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, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
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 / SPI-1 type 3 secretion system needle filament protein / Protein PrgJ
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
DepositionJun 20, 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
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
A: Protein InvG
AM: Protein PrgJ
AN: Protein PrgJ
AO: Protein PrgJ
AP: Protein PrgJ
AQ: Protein PrgJ
AR: Protein PrgJ
AS: Protein PrgI
AT: Protein PrgI
AU: Protein PrgI
AV: Protein PrgI
AW: Protein PrgI
AX: Protein PrgI
AY: Protein PrgI
AZ: Protein PrgI
B: Protein InvG
BA: Protein PrgI
BB: Protein PrgI
BC: Protein PrgI
BD: Protein PrgI
BE: Protein PrgI
C: Protein InvG
D: Protein InvG
E: Protein PrgH
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
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
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


Theoretical massNumber of molelcules
Total (without water)2,430,64469
Polymers2,430,64469
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: 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
#2: 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
#3: 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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Protein , 4 types, 59 molecules ABCDFGHIJKLMNOPQAMANAOAPAQARASATAUAVAWAXAYAZ...

#4: 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
#5: Protein
Protein PrgJ


Mass: 10934.425 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P41785
#6: Protein
Protein PrgI


Mass: 8864.868 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P41784
#7: 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

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Details

Has protein modificationY

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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: Focussed refinement of InvGN0N1:SpaPQR:PrgIJ from the Salmonella SPI-1 injectisome needle complex
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.5 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
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 FIELD
Image recordingElectron dose: 51.3 e/Å2 / Detector mode: SUPER-RESOLUTION / 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: 25666 / Symmetry type: POINT

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