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- EMDB-4734: Structure of the core Shigella flexneri type III secretion system... -

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Basic information

Entry
Database: EMDB / ID: EMD-4734
TitleStructure of the core Shigella flexneri type III secretion system export gate complex SctRST (Spa24/Spa9/Spa29).Type three secretion system
Map data
Sample
  • Complex: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)Type three secretion system
    • 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
Function / homology
Function and homology information


protein secretion / protein targeting / 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 / FliP family / Flagella transport protein fliP family signature 2.
Similarity search - Domain/homology
Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaQ / Surface presentation of antigens protein SpaR
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJohnson S / Kuhlen L / Deme JC / Abrusci P / Lea SM
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M011984 United Kingdom
Wellcome Trust109136 United Kingdom
Wellcome Trust201536 United Kingdom
Wolfson FoundationWL160052 United Kingdom
Wellcome Trust201536 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of the core of the type III secretion system export apparatus.
Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / ...Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / Carol V Robinson / Susan M Lea /
Abstract: Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are ...Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. Here, we present the cryoelectron microscopy structure of the Salmonella Typhimurium FliP-FliQ-FliR complex at 4.2 Å. None of the subunits adopt canonical integral membrane protein topologies, and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.
History
DepositionMar 26, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseMay 29, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing 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-6r6b
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4734.png

Downloads & links

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Map

FileDownload / File: emd_4734.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.009494857 - 0.029651769
Average (Standard dev.)0.00000022428 (±0.0014135778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.73601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z236.736236.736236.736
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0090.0300.000

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Supplemental data

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Mask #1

Fileemd_4734_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_4734_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4734_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4734_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)

EntireName: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)Type three secretion system
Components
  • Complex: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)Type three secretion system
    • 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

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Supramolecule #1: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)

SupramoleculeName: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Shigella flexneri (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: MT56
Molecular weightExperimental: 191 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: Shigella flexneri (bacteria)
Molecular weightTheoretical: 24.215562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLSDMSLIAT LSFFTLLPFL VAAGTCYIKF SIVFVMVRNA LGLQQVPSNM TLNGIALIMA LFVMKPIIEA GYENYLNGPQ KFDTISDIV RFSDSGLMEY KQYLKKHTDL ELARFFQRSE EENADLKSAE NNDYSLFSLL PAYALSEIKD AFKIGFYLYL P FVVVDLVI ...String:
MLSDMSLIAT LSFFTLLPFL VAAGTCYIKF SIVFVMVRNA LGLQQVPSNM TLNGIALIMA LFVMKPIIEA GYENYLNGPQ KFDTISDIV RFSDSGLMEY KQYLKKHTDL ELARFFQRSE EENADLKSAE NNDYSLFSLL PAYALSEIKD AFKIGFYLYL P FVVVDLVI SSILLALGMM MMSPITISVP IKLVLFVALD GWGILSKALI EQYINIPA

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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: Shigella flexneri (bacteria)
Molecular weightTheoretical: 32.644086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDISSWFESI HVFLILLNGV FFRLAPLFFF LPFLNNGIIS PSIRIPVIFL VASGLITSGK VDIGSSVFEH VYFLMFKEII VGLLLSFCL SLPFWIFHAV GSIIDNQRGA TLSSSIDPAN GVDTSELAKF FNLFSAVVFL YSGGMVFILE SIQLSYNICP L FSQCSFRI ...String:
MDISSWFESI HVFLILLNGV FFRLAPLFFF LPFLNNGIIS PSIRIPVIFL VASGLITSGK VDIGSSVFEH VYFLMFKEII VGLLLSFCL SLPFWIFHAV GSIIDNQRGA TLSSSIDPAN GVDTSELAKF FNLFSAVVFL YSGGMVFILE SIQLSYNICP L FSQCSFRI SNILTFLTLL ASQAVILASP VMIVLLLSEV LLGVLSRFAP QMNAFSVSLT IKSLLAIFII FICSSTIYFS KV QFFLGEH KFFTNLFVRE NLYFQGQFGS WSHPQFEKGG GSGGGSGGGS WSHPQFEK

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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: Shigella flexneri (bacteria)
Molecular weightTheoretical: 9.433338 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSDIVYMGNK ALYLILIFSL WPVGIATVIG LSIGLLQTVT QLQEQTLPFG IKLIGVSISL LLLSGWYGEV LLSFCHEIMF LIKSGV

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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

Concentration8.4 mg/mL
BufferpH: 8
Component:
ConcentrationName
100.0 mMTris
150.0 mMsodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3741 / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 775073
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.8)
Startup modelType of model: EMDB MAP
EMDB ID:

4173


Details: 40 angstrom low pass filtered
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 212561
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6r6b:
Structure of the core Shigella flexneri type III secretion system export gate complex SctRST (Spa24/Spa9/Spa29).

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