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- EMDB-11780: Apo-state type 3 secretion system export apparatus complex from S... -

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Basic information

Entry
Database: EMDB / ID: EMD-11780
TitleApo-state type 3 secretion system export apparatus complex from Salmonella enterica typhimurium
Map dataPostprocess Bfactor: -30
Sample
  • Complex: Export apparatus core complex with inner rod and needle filament proteins PrgJ and PrgI.
    • Protein or peptide: Surface presentation of antigens protein SpaP
    • Protein or peptide: Surface presentation of antigens protein SpaR
    • Protein or peptide: Surface presentation of antigens protein SpaQ
    • Protein or peptide: Protein PrgJ
    • Protein or peptide: Protein PrgI
Function / homology
Function and homology information


The IPAF inflammasome / type III protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / protein transport / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein ...: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / 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
Surface presentation of antigens protein SpaQ / Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaR / SPI-1 type 3 secretion system needle filament protein / Protein PrgJ
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGoessweiner-Mohr N / Fahrenkamp D / Miletic S / Wald J / Marlovits T
Funding support Austria, Germany, 2 items
OrganizationGrant numberCountry
Austrian Science FundI 2408-B22 Austria
German Research Foundation (DFG)FA1518/2-1 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation.
Authors: Sean Miletic / Dirk Fahrenkamp / Nikolaus Goessweiner-Mohr / Jiri Wald / Maurice Pantel / Oliver Vesper / Vadim Kotov / Thomas C Marlovits /
Abstract: Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome ...Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
History
DepositionSep 23, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7agx
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7agx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11780.png

Downloads & links

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Map

FileDownload / File: emd_11780.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess Bfactor: -30
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.01
Minimum - Maximum-0.06106985 - 0.0872564
Average (Standard dev.)-0.0002593318 (±0.0032711106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 470.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z470.880470.880470.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0610.087-0.000

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Supplemental data

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Additional map: Refine3D

Fileemd_11780_additional_1.map
AnnotationRefine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11780_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11780_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Export apparatus core complex with inner rod and needle filament ...

EntireName: Export apparatus core complex with inner rod and needle filament proteins PrgJ and PrgI.
Components
  • Complex: Export apparatus core complex with inner rod and needle filament proteins PrgJ and PrgI.
    • Protein or peptide: Surface presentation of antigens protein SpaP
    • Protein or peptide: Surface presentation of antigens protein SpaR
    • Protein or peptide: Surface presentation of antigens protein SpaQ
    • Protein or peptide: Protein PrgJ
    • Protein or peptide: Protein PrgI

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Supramolecule #1: Export apparatus core complex with inner rod and needle filament ...

SupramoleculeName: Export apparatus core complex with inner rod and needle filament proteins PrgJ and PrgI.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Apo-state
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Location in cell: Membrane
Molecular weightTheoretical: 336 KDa

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Macromolecule #1: Surface presentation of antigens protein SpaP

MacromoleculeName: Surface presentation of antigens protein SpaP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 25.249596 KDa
SequenceString: MGNDISLIAL LAFSTLLPFI IASGTCFVKF SIVFVMVRNA LGLQQIPSNM TLNGVALLLS MFVMWPIMHD AYVYFEDEDV TFNDISSLS KHVDEGLDGY RDYLIKYSDR ELVQFFENAQ LKRQYGEETE TVKRDKDEIE KPSIFALLPA YALSEIKSAF K IGFYLYLP ...String:
MGNDISLIAL LAFSTLLPFI IASGTCFVKF SIVFVMVRNA LGLQQIPSNM TLNGVALLLS MFVMWPIMHD AYVYFEDEDV TFNDISSLS KHVDEGLDGY RDYLIKYSDR ELVQFFENAQ LKRQYGEETE TVKRDKDEIE KPSIFALLPA YALSEIKSAF K IGFYLYLP FVVVDLVVSS VLLALGMMMM SPVTISTPIK LVLFVALDGW TLLSKGLILQ YMDIAT

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Macromolecule #2: Surface presentation of antigens protein SpaR

MacromoleculeName: Surface presentation of antigens protein SpaR / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 28.499533 KDa
SequenceString: MFYALYFEIH HLVASAALGF ARVAPIFFFL PFLNSGVLSG APRNAIIILV ALGVWPHALN EAPPFLSVAM IPLVLQEAAV GVMLGCLLS WPFWVMHALG CIIDNQRGAT LSSSIDPANG IDTSEMANFL NMFAAVVYLQ NGGLVTMVDV LNKSYQLCDP M NECTPSLP ...String:
MFYALYFEIH HLVASAALGF ARVAPIFFFL PFLNSGVLSG APRNAIIILV ALGVWPHALN EAPPFLSVAM IPLVLQEAAV GVMLGCLLS WPFWVMHALG CIIDNQRGAT LSSSIDPANG IDTSEMANFL NMFAAVVYLQ NGGLVTMVDV LNKSYQLCDP M NECTPSLP PLLTFINQVA QNALVLASPV VLVLLLSEVF LGLLSRFAPQ MNAFAISLTV KSGIAVLIML LYFSPVLPDN VL RLSFQAT GLSSWFYERG ATHVLE

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Macromolecule #3: Surface presentation of antigens protein SpaQ

MacromoleculeName: Surface presentation of antigens protein SpaQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 9.363229 KDa
SequenceString:
MDDLVFAGNK ALYLVLILSG WPTIVATIIG LLVGLFQTVT QLQEQTLPFG IKLLGVCLCL FLLSGWYGEV LLSYGRQVIF LALAKG

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Macromolecule #4: Protein PrgJ

MacromoleculeName: Protein PrgJ / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 10.934425 KDa
SequenceString:
MSIATIVPEN AVIGQAVNIR SMETDIVSLD DRLLQAFSGS AIATAVDKQT ITNRIEDPNL VTDPKELAIS QEMISDYNLY VSMVSTLTR KGVGAVETLL RS

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Macromolecule #5: Protein PrgI

MacromoleculeName: Protein PrgI / type: protein_or_peptide / ID: 5 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 8.864868 KDa
SequenceString:
MATPWSGYLD DVSAKFDTGV DNLQTQVTEA LDKLAAKPSD PALLAAYQSK LSEYNLYRNA QSNTVKVFKD IDAAIIQNFR

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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: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 31.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Rotationally averaged 3D structure
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54491
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7agx:
Apo-state type 3 secretion system export apparatus complex from Salmonella enterica typhimurium

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