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- EMDB-8914: Structure of the Salmonella SPI-1 type III secretion injectisome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8914
TitleStructure of the Salmonella SPI-1 type III secretion injectisome secretin InvG in the open gate state
Map dataSalmonella SPI-1 type III secretion injectisome secretin InvG in the open gate state
Sample
  • Complex: Salmonella SPI-1 type III secretion injectisome secretin oligomer
    • Protein or peptide: Protein InvG
KeywordsType III secretion system / secretin / MEMBRANE PROTEIN
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
: / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHu J / Worrall LJ
Funding support Canada, United States, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.
Authors: J Hu / L J Worrall / C Hong / M Vuckovic / C E Atkinson / N Caveney / Z Yu / N C J Strynadka /
Abstract: The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome ...The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.
History
DepositionJun 22, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseOct 3, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dv3
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8914.png

Downloads & links

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Map

FileDownload / File: emd_8914.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalmonella SPI-1 type III secretion injectisome secretin InvG in the open gate state
Voxel sizeX=Y=Z: 1.75 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.78894496 - 0.9376523
Average (Standard dev.)0.00041115415 (±0.020050945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 525.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z525.000525.000525.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.7890.9380.000

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Supplemental data

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Sample components

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Entire : Salmonella SPI-1 type III secretion injectisome secretin oligomer

EntireName: Salmonella SPI-1 type III secretion injectisome secretin oligomer
Components
  • Complex: Salmonella SPI-1 type III secretion injectisome secretin oligomer
    • Protein or peptide: Protein InvG

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Supramolecule #1: Salmonella SPI-1 type III secretion injectisome secretin oligomer

SupramoleculeName: Salmonella SPI-1 type III secretion injectisome secretin oligomer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Protein InvG

MacromoleculeName: Protein InvG / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 61.835559 KDa
SequenceString: MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKITG NFEFHDPNAL LEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL NEFNNFLKRS GLYNKNYPLR GDNRKGTFYV SGPPVYVDMV V NAATMMDK ...String:
MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKITG NFEFHDPNAL LEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL NEFNNFLKRS GLYNKNYPLR GDNRKGTFYV SGPPVYVDMV V NAATMMDK QNDGIELGRQ KIGVMRLNNT FVGDRTYNLR DQKMVIPGIA TAIERLLQGE EQPLGNIVSS EPPAMPAFSA NG EKGKAAN YAGGMSLQEA LKQNAAAGNI KIVAYPDTNS LLVKGTAEQV HFIEMLVKAL DVAKRHVELS LWIVDLNKSD LER LGTSWS GSITIGDKLG VSLNQSSIST LDGSRFIAAV NALEEKKQAT VVSRPVLLTQ ENVPAIFDNN RTFYTKLIGE RNVA LEHVT YGTMIRVLPR FSADGQIEMS LDIEDGNDKT PQSDTTTSVD ALPEVGRTLI STIARVPHGK SLLVGGYTRD ANTDT VQSI PFLGKLPLIG SLFRYSSKNK SNVVRVFMIE PKEIVDPLTP DASESVNNIL KQSGAWSGDD KLQKWVRVYL DRGQEA IK

UniProtKB: SPI-1 type 3 secretion system secretin

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 80000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.01) / Number images used: 26000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.01)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.01)

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