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- PDB-9vko: CryoEM struccture of the type III secretion system gatekeeper pro... -

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Basic information

Entry
Database: PDB / ID: 9vko
TitleCryoEM struccture of the type III secretion system gatekeeper protein InvE by cryo-electron microscopy.
ComponentsInvasion protein InvE
KeywordsCYTOSOLIC PROTEIN / tetramer / T3SS / gatekeeper / Regulation of Protein Secretion Order
Function / homology
Function and homology information


outer membrane / protein secretion by the type III secretion system / 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 str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsCheng, X.Q. / Wu, M. / Jiang, W.X. / Xing, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371277 China
National Natural Science Foundation of China (NSFC)32301028 China
CitationJournal: To Be Published
Title: CryoEM struccture of the type III secretion system gatekeeper protein InvE by cryo-electron microscopy.
Authors: Cheng, X.Q. / Wu, M. / Jiang, W.X. / Xing, Q.
History
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

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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)169,9024
Polymers169,9024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Invasion protein InvE


Mass: 42475.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: SR-11 LT2 / SGSC1412 / ATCC 700720 TML / 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: Invasion protein InvE / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 135.6 kDa/nm / Experimental value: NO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris1
2200 mMsodium chlorideNaCl1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
3EPU9.03image acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213045 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049732
ELECTRON MICROSCOPYf_angle_d0.51313120
ELECTRON MICROSCOPYf_dihedral_angle_d4.1711296
ELECTRON MICROSCOPYf_chiral_restr0.0351512
ELECTRON MICROSCOPYf_plane_restr0.0041652

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