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- PDB-9y93: Tetrameric InvE from Salmonella Typhimurium -

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Basic information

Entry
Database: PDB / ID: 9y93
TitleTetrameric InvE from Salmonella Typhimurium
ComponentsInvasion protein InvE
KeywordsPROTEIN TRANSPORT / tetramer / gatekeeper protein / T3SS
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / cell surface / plasma membrane
Similarity search - Function
Salmonella/Shigella invasion protein E / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain
Similarity search - Domain/homology
Invasion protein InvE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsZhu, L.Y. / Wang, T.T. / Guo, E.Z. / Lara-Tejero, M. / Galan, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI030492 United States
CitationJournal: To Be Published
Title: Oligomeric Assembly of the Gatekeeper InvE Orchestrates Hierarchical Type III Protein Secretion in Salmonella Typhimurium
Authors: Wang, T.T. / Zhu, L.Y. / Guo, E.Z. / Lara-Tejero, M. / Galan, J.E.
History
DepositionSep 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Invasion protein InvE
B: Invasion protein InvE
C: Invasion protein InvE
D: Invasion protein InvE


Theoretical massNumber of molelcules
Total (without water)182,1554
Polymers182,1554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, light scattering, SEC-MALS were performed to measure the molecular weight of the InvE oligomer., cross-linking, DSS chemical crosslink and ...Evidence: electron microscopy, not applicable, light scattering, SEC-MALS were performed to measure the molecular weight of the InvE oligomer., cross-linking, DSS chemical crosslink and photocrosslink were performed to confirm its molecular weight in SDS-PAGE gel.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Invasion protein InvE


Mass: 45538.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: invE, STM2897 / Production host: Escherichia coli (E. coli) / References: UniProt: P35671
Has protein modificationN

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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: InvE / Type: COMPLEX
Details: In Salmonella enterica serovar Typhimurium, the SPI 1 gatekeeper InvE governs the hierarchical secretion of T3SS substrates. Here InvE forms a homotetramer. Its oligomeric assemblies is essential for function.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC4.4.13D reconstructionlocal refinement job was used to generate the final map
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2169983 / Symmetry type: POINT
RefinementHighest resolution: 2.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039252
ELECTRON MICROSCOPYf_angle_d0.4312484
ELECTRON MICROSCOPYf_dihedral_angle_d3.3521224
ELECTRON MICROSCOPYf_chiral_restr0.0331435
ELECTRON MICROSCOPYf_plane_restr0.0031569

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