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- PDB-3j1x: A refined model of the prototypical Salmonella typhimurium T3SS b... -

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Basic information

Entry
Database: PDB / ID: 3j1x
TitleA refined model of the prototypical Salmonella typhimurium T3SS basal body reveals the molecular basis for its assembly
ComponentsProtein PrgH
KeywordsCELL INVASION / T3SS
Function / homologyType III secretion system, PrgH/EprH / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / plasma membrane / Protein PrgH
Function and homology information
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. / Worrall, L.J. / Strynadka, N.C.J. / 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 10, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 0THIS ENTRY 3J1X CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ...THIS ENTRY 3J1X 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

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-1875
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Structure viewerMolecule:
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Assembly

Deposited unit
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: Protein PrgH
P: Protein PrgH
Q: Protein PrgH
R: Protein PrgH
S: Protein PrgH
T: Protein PrgH
U: Protein PrgH
V: Protein PrgH
W: Protein PrgH
X: Protein PrgH


Theoretical massNumber of molelcules
Total (without water)537,20124
Polymers537,20124
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 PrgH


Mass: 22383.385 Da / Num. of mol.: 24 / Fragment: UNP residues 173-363 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P41783

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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
2Salmonella T3SS 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: C24 (24 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
Atomic model buildingPDB-ID: 4G1I

4g1i


Accession code: 4G1I / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms37896 0 0 0 37896

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