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- EMDB-4173: A FliPQR complex forms the core of the Salmonella type III secret... -

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Basic information

Entry
Database: EMDB / ID: EMD-4173
TitleA FliPQR complex forms the core of the Salmonella type III secretion system export apparatus.
Map dataPost-processed (B-factor sharpened and masked) map
Sample
  • Complex: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliR
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
KeywordsT3SS / Flagella / Cryo-EM / Export / Membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / 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
Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica (bacteria) / Salmonella enterica subsp. enterica (bacteria) / Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsJohnson S / Kuhlen L
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M011984 United Kingdom
Wellcome Trust100298 United Kingdom
Wellcome Trust201536 United Kingdom
Wolfson FoundationWL160052 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
DepositionNov 24, 2017-
Header (metadata) releaseDec 6, 2017-
Map releaseJul 4, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f2d
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4173.png

Downloads & links

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Map

FileDownload / File: emd_4173.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (B-factor sharpened and masked) map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.1337746 - 0.2577469
Average (Standard dev.)0.002151701 (±0.012342309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1340.2580.002

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Supplemental data

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Half map: Half map 1

Fileemd_4173_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_4173_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the flagellar type III secretion system export apparat...

EntireName: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliR
Components
  • Complex: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliR
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ

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Supramolecule #1: Complex of the flagellar type III secretion system export apparat...

SupramoleculeName: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 195 kDa/nm

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Macromolecule #1: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica (bacteria)
Molecular weightTheoretical: 26.769021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ...String:
MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ILLPAYVTSE LKTAFQIGFT IFIPFLIIDL VIASVLMALG MMMVPPATIA LPFKLMLFVL VDGWQLLVGS LA QSFYS

UniProtKB: Flagellar biosynthetic protein FliP

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Macromolecule #2: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 2
Details: Residues 265 onwards constitute the Twin-Strep tag used for purification
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 33.06918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA ...String:
MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA FMALARAGGL IFLNGLMLAL PVITLLLTLN LALGLLNRMA PQLSIFVIGF PLTLTVGIML MAALMPLIAP FC EHLFSEI FNLLADIVSE MPINNNPENL YFQGQFGSWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Flagellar biosynthetic protein FliR

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Macromolecule #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 9.606758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG

UniProtKB: Flagellar biosynthetic protein FliQ

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number real images: 401 / #0 - Average electron dose: 47.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Number real images: 1687 / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID2
DetailsImages from K2 were also added.
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 97718
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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