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- EMDB-24735: Cryo-EM structure of the needle filament-tip complex of the Salmo... -

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Basic information

Entry
Database: EMDB / ID: EMD-24735
TitleCryo-EM structure of the needle filament-tip complex of the Salmonella type III secretion injectisomeType three secretion system
Map dataNeedle filament-tip complex of the Salmonella type III secretion injectisomeType three secretion system
Sample
  • Complex: The needle complex with tip
    • Protein or peptide: Protein PrgI
    • Protein or peptide: Cell invasion protein SipD
Keywordsprotein secretion / bacterial pathogenesis / organelle assembly / CELL INVASION
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 systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / 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
Cell invasion protein SipD / SPI-1 type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGuo EZ / Galan JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI030492 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structure of the needle filament tip complex of the type III secretion injectisome.
Authors: Emily Z Guo / Jorge E Galán /
Abstract: Type III secretion systems are multiprotein molecular machines required for the virulence of several important bacterial pathogens. The central element of these machines is the injectisome, a ∼5-Md ...Type III secretion systems are multiprotein molecular machines required for the virulence of several important bacterial pathogens. The central element of these machines is the injectisome, a ∼5-Md multiprotein structure that mediates the delivery of bacterially encoded proteins into eukaryotic target cells. The injectisome is composed of a cytoplasmic sorting platform, and a membrane-embedded needle complex, which is made up of a multiring base and a needle-like filament that extends several nanometers from the bacterial surface. The needle filament is capped at its distal end by another substructure known as the tip complex, which is crucial for the translocation of effector proteins through the eukaryotic cell plasma membrane. Here we report the cryo-EM structure of the Typhimurium needle tip complex docked onto the needle filament tip. Combined with a detailed analysis of structurally guided mutants, this study provides major insight into the assembly and function of this essential component of the type III secretion protein injection machine.
History
DepositionAug 25, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rye
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24735.png

Downloads & links

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Map

FileDownload / File: emd_24735.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeedle filament-tip complex of the Salmonella type III secretion injectisome
Voxel sizeX=Y=Z: 1.715 Å
Density
Contour LevelBy AUTHOR: 0.0435 / Movie #1: 0.0435
Minimum - Maximum-0.0940567 - 0.17814146
Average (Standard dev.)0.0005739318 (±0.0063521964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 308.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7151.7151.715
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z308.700308.700308.700
α/β/γ90.00090.00090.000
start NX/NY/NZ45440
NX/NY/NZ103105148
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0940.1780.001

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Supplemental data

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Sample components

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Entire : The needle complex with tip

EntireName: The needle complex with tip
Components
  • Complex: The needle complex with tip
    • Protein or peptide: Protein PrgI
    • Protein or peptide: Cell invasion protein SipD

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Supramolecule #1: The needle complex with tip

SupramoleculeName: The needle complex with tip / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SL1344

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Macromolecule #1: Protein PrgI

MacromoleculeName: Protein PrgI / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 8.864868 KDa
SequenceString:
MATPWSGYLD DVSAKFDTGV DNLQTQVTEA LDKLAAKPSD PALLAAYQSK LSEYNLYRNA QSNTVKVFKD IDAAIIQNFR

UniProtKB: SPI-1 type 3 secretion system needle filament protein

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Macromolecule #2: Cell invasion protein SipD

MacromoleculeName: Cell invasion protein SipD / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 37.141148 KDa
SequenceString: MLNIQNYSAS PHPGIVAERP QTPSASEHVE TAVVPSTTEH RGTDIISLSQ AATKIHQAQQ TLQSTPPISE ENNDERTLAR QQLTSSLNA LAKSGVSLSA EQNENLRSAF SAPTSALFSA SPMAQPRTTI SDAEIWDMVS QNISAIGDSY LGVYENVVAV Y TDFYQAFS ...String:
MLNIQNYSAS PHPGIVAERP QTPSASEHVE TAVVPSTTEH RGTDIISLSQ AATKIHQAQQ TLQSTPPISE ENNDERTLAR QQLTSSLNA LAKSGVSLSA EQNENLRSAF SAPTSALFSA SPMAQPRTTI SDAEIWDMVS QNISAIGDSY LGVYENVVAV Y TDFYQAFS DILSKMGGWL LPGKDGNTVK LDVTSLKNDL NSLVNKYNQI NSNTVLFPAQ SGSGVKVATE AEARQWLSEL NL PNSCLKS YGSGYVVTVD LTPLQKMVQD IDGLGAPGKD SKLEMDNAKY QAWQSGFKAQ EENMKTTLQT LTQKYSNANS LYD NLVKVL SSTISSSLET AKSFLQG

UniProtKB: Cell invasion protein SipD

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTris-HClTrisTris Hydrochloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa / Details: 25 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20046

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 27737

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT / Overall B value: 85
Output model

PDB-7rye:
Cryo-EM structure of the needle filament-tip complex of the Salmonella type III secretion injectisome

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