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- PDB-6dwb: Structure of the Salmonella SPI-1 type III secretion injectisome ... -

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Basic information

Entry
Database: PDB / ID: 6dwb
TitleStructure of the Salmonella SPI-1 type III secretion injectisome needle filament
ComponentsProtein PrgI
KeywordsMEMBRANE PROTEIN / Type III secretion system
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
SPI-1 type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHu, J. / Hong, C. / Worrall, L.J. / Vuckovic, M. / Yu, Z. / Strynadka, N.C.J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.
Authors: J Hu / L J Worrall / C Hong / M Vuckovic / C E Atkinson / N Caveney / Z Yu / N C J Strynadka /
Abstract: The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome ...The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Protein PrgI
B: Protein PrgI
C: Protein PrgI
D: Protein PrgI
E: Protein PrgI
F: Protein PrgI
G: Protein PrgI
H: Protein PrgI
I: Protein PrgI
J: Protein PrgI
K: Protein PrgI
L: Protein PrgI
M: Protein PrgI
N: Protein PrgI
O: Protein PrgI
P: Protein PrgI
Q: Protein PrgI
R: Protein PrgI
S: Protein PrgI
T: Protein PrgI
U: Protein PrgI
V: Protein PrgI
W: Protein PrgI
X: Protein PrgI
Y: Protein PrgI
Z: Protein PrgI
a: Protein PrgI
b: Protein PrgI
c: Protein PrgI
d: Protein PrgI


Theoretical massNumber of molelcules
Total (without water)265,94630
Polymers265,94630
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area95310 Å2
ΔGint-529 kcal/mol
Surface area91750 Å2

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Components

#1: Protein ...
Protein PrgI


Mass: 8864.868 Da / Num. of mol.: 30 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P41784

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PrgI helical filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Nominal magnification: 81000 X / Calibrated magnification: 37037 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1100 nm / Calibrated defocus max: 2600 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3753
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Spherical aberration corrector: Cs corrector was used.
Image scansSampling size: 5 µm / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
2SerialEM3.6image acquisition
4CTFFINDCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 88687
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00718690
ELECTRON MICROSCOPYf_angle_d0.52925440
ELECTRON MICROSCOPYf_dihedral_angle_d2.63111340
ELECTRON MICROSCOPYf_chiral_restr0.0362910
ELECTRON MICROSCOPYf_plane_restr0.0053330

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