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- PDB-3j1v: A refined model of the prototypical Salmonella typhimurium T3SS b... -

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Basic information

Entry
Database: PDB / ID: 3j1v
TitleA refined model of the prototypical Salmonella typhimurium T3SS basal body reveals the molecular basis for its assembly
ComponentsProtein InvG
KeywordsCELL INVASION / T3SS / Secretin
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 / cell outer membrane / identical protein binding
Similarity search - Function
: / 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 / 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
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsSgourakis, N.G. / Bergeron, J.R.C. / Strynadka, N.J.C. / Baker, D.
CitationJournal: Science / Year: 2011
Title: Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Authors: Oliver Schraidt / Thomas C Marlovits /
Abstract: Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core ...Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.
History
DepositionJul 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 3J1V CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ...THIS ENTRY 3J1V CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ORIGINALLY BY AUTHORS: O.SCHRAIDT, T.C.MARLOVITS

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: Protein InvG
B: Protein InvG
C: Protein InvG
D: Protein InvG
E: 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


Theoretical massNumber of molelcules
Total (without water)265,41315
Polymers265,41315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protein InvG


Mass: 17694.172 Da / Num. of mol.: 15 / Fragment: UNP residues 22-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: invG, STM2898 / Production host: Escherichia coli (E. coli) / References: UniProt: P35672

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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

Component
IDNameTypeParent-ID
1Salmonella typhimurium T3SS basal bodyCOMPLEX0
2T3SS injectisome1
Buffer solutionpH: 7.5 / Details: 10mM Tris-HCl (pH 7.5) 0.5mM NaCl 0.1% LDAO
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 93000 X
Image recordingFilm or detector model: GENERIC CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Rosettamodel fitting
2IMAGIC3D reconstruction
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 11.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37171 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms16650 0 0 0 16650

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