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- PDB-6ofe: Helical reconstruction of Type III Secretion System Needle filame... -

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Basic information

Database: PDB / ID: 6ofe
TitleHelical reconstruction of Type III Secretion System Needle filament mutant-PrgI S49A
ComponentsProtein PrgI
KeywordsPROTEIN TRANSPORT / Type III secretion / helical reconstruction / PrgI filament / salmonella
Function / homology
Function and homology information

type III protein secretion system complex / protein secretion by the type III secretion system / pathogenesis / identical protein binding
Type III secretion system, needle protein / 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 apparatus / Protein PrgI
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.61 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.
Validation Report
SummaryFull reportAbout validation report
DepositionMar 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Deposited unit
P: Protein PrgI
Q: Protein PrgI
R: Protein PrgI
S: Protein PrgI
T: Protein PrgI
K: Protein PrgI
L: Protein PrgI
M: Protein PrgI
N: Protein PrgI
O: Protein PrgI
F: Protein PrgI
G: Protein PrgI
H: Protein PrgI
I: Protein PrgI
J: Protein PrgI
D: Protein PrgI
A: Protein PrgI
B: Protein PrgI
C: Protein PrgI
E: Protein PrgI

Theoretical massNumber of molelcules
Total (without water)182,62320

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54950 Å2
ΔGint-293 kcal/mol
Surface area66300 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 4.19 Å / Rotation per n subunits: 63.35 °)


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

Mass: 9131.145 Da / Num. of mol.: 20 / Mutation: S49A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: prgI, SL1344_2853 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NF82, UniProt: P41784*PLUS

Experimental details


EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

ComponentName: PrgI S49A / Type: COMPLEX / Details: single mutant of PrgI / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Salmonella typhimurium (strain SL1344) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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 FIELDBright-field microscopy
Image recordingElectron dose: 47.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
Helical symmertyAngular rotation/subunit: 63.35 ° / Axial rise/subunit: 4.19 Å / Axial symmetry: C1
3D reconstructionResolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14070 / Symmetry type: HELICAL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612440
ELECTRON MICROSCOPYf_angle_d0.61516940
ELECTRON MICROSCOPYf_dihedral_angle_d3.7287540
ELECTRON MICROSCOPYf_chiral_restr0.0411940
ELECTRON MICROSCOPYf_plane_restr0.0052220

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