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- PDB-6ofh: Structure of Salmonella type III secretion system needle filament -

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Basic information

Entry
Database: PDB / ID: 6ofh
TitleStructure of Salmonella type III secretion system needle filament
ComponentsProtein PrgI
KeywordsPROTEIN TRANSPORT / type III secretion system / salmonella / helical reconstruction
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
Type III secretion system apparatus / SPI-1 type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGuo, E.Z. / 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: PLoS Biol / Year: 2019
Title: A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.
Authors: Emily Z Guo / Daniel C Desrosiers / Jan Zalesak / James Tolchard / Mélanie Berbon / Birgit Habenstein / Thomas Marlovits / Antoine Loquet / Jorge E Galán /
Abstract: Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines ...Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines is the injectisome, a multiprotein complex that mediates the selection of substrates, their passage through the bacterial envelope, and ultimately their delivery into eukaryotic target cells. The injectisome is composed of a large cytoplasmic complex or sorting platform, a multiring base embedded in the bacterial envelope, and a needle-like filament that protrudes several nanometers from the bacterial surface and is capped at its distal end by the tip complex. A characteristic feature of these machines is that their activity is stimulated by contact with target host cells. The sensing of target cells, thought to be mediated by the distal tip of the needle filament, generates an activating signal that must be transduced to the secretion machine by the needle filament. Here, through a multidisciplinary approach, including solid-state NMR (SSNMR) and cryo electron microscopy (cryo-EM) analyses, we have identified critical residues of the needle filament protein of a Salmonella Typhimurium type III secretion system that are involved in the regulation of the activity of the secretion machine. We found that mutations in the needle filament protein result in various specific phenotypes associated with different steps in the type III secretion process. More specifically, these studies reveal an important role for a polymorphic helix of the needle filament protein and the residues that line the lumen of its central channel in the control of type III secretion.
History
DepositionMar 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 10, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
D: Protein PrgI
U: Protein PrgI
V: 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


Theoretical massNumber of molelcules
Total (without water)168,43219
Polymers168,43219
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51120 Å2
ΔGint-302 kcal/mol
Surface area65360 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 19 / Rise per n subunits: 4.24 Å / Rotation per n subunits: 63.35 °)

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Components

#1: Protein
Protein PrgI / Type III secretion system apparatus


Mass: 8864.868 Da / Num. of mol.: 19 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / References: UniProt: A0A0H3NF82, UniProt: P41784*PLUS
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: filament structure of PrgI needle attached to the base
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella typhimurium (strain SL1344) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 63.35 ° / Axial rise/subunit: 4.24 Å / Axial symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53866 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00611837
ELECTRON MICROSCOPYf_angle_d0.62816112
ELECTRON MICROSCOPYf_dihedral_angle_d3.2657182
ELECTRON MICROSCOPYf_chiral_restr0.0391843
ELECTRON MICROSCOPYf_plane_restr0.0052109

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