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- EMDB-6917: cryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6917
TitlecryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex
Map datasharpening map
Sample
  • Complex: Pilotin-Secretin Complex Asps-GspD
    • Protein or peptide: Type II secretion system protein D
    • Protein or peptide: Type II secretion system lipoprotein
KeywordsPilotin / Secretin / PROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane
Similarity search - Function
Type II secretion system (T2SS) pilotin, S protein / Type II secretion system (T2SS) pilotin, S protein / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain ...Type II secretion system (T2SS) pilotin, S protein / Type II secretion system (T2SS) pilotin, S protein / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Secretin GspD 2 / Pilotin AspS 2
Similarity search - Component
Biological speciesEscherichia coli ETEC H10407 (bacteria) / Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin M / Yan Z
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural insight into the assembly of the type II secretion system pilotin-secretin complex from enterotoxigenic Escherichia coli.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li /
Abstract: Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II ...Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II secretion system, a lipoprotein called pilotin is essential to bind and target its corresponding secretin to the outer membrane. However, there is only limited structural information available about the interaction and assembly of the pilotin-secretin complex. Here we report the first near-atomic-resolution structure of a full-length Vibrio-type pilotin-secretin (AspS-GspD) complex from enterotoxigenic Escherichia coli by cryo-electron microscopy, which reveals the detailed assembly mode of the full-length pilotin-secretin complex. The AspS subunits attach to the secretin channel surface with a 15:15 stoichiometric ratio to GspD subunits, and insert their amino terminus into the outer membrane. The AspS subunits interact with all three secondary structural elements of the S domain of GspD, including strong interaction with the carboxy-terminal α-helix and weak interactions with another two elements, an α-helix and a loop. These structural and biochemical details provide a deeper insight to pilotin-secretin interaction and their assembly mode.
History
DepositionFeb 23, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseApr 18, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zdh
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6917.png

Downloads & links

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Map

FileDownload / File: emd_6917.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.13690214 - 0.27743185
Average (Standard dev.)0.0003305285 (±0.006083185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1370.2770.000

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Supplemental data

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Sample components

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Entire : Pilotin-Secretin Complex Asps-GspD

EntireName: Pilotin-Secretin Complex Asps-GspD
Components
  • Complex: Pilotin-Secretin Complex Asps-GspD
    • Protein or peptide: Type II secretion system protein D
    • Protein or peptide: Type II secretion system lipoprotein

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Supramolecule #1: Pilotin-Secretin Complex Asps-GspD

SupramoleculeName: Pilotin-Secretin Complex Asps-GspD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)

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Macromolecule #1: Type II secretion system protein D

MacromoleculeName: Type II secretion system protein D / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC
Molecular weightTheoretical: 69.70082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEATFTANFK DTDLKSFIET VGANLNKTII MGPGVQGKVS IRTMTPLNER QYYQLFLNLL EAQGYAVVPM ENDVLKVVKS SAAKVEPLP LVGEGSDNYA GDEMVTKVVP VRNVSVRELA PILRQMIDSA GSGNVVNYDP SNVIMLTGRA SVVERLTEVI Q RVDHAGNR ...String:
EEATFTANFK DTDLKSFIET VGANLNKTII MGPGVQGKVS IRTMTPLNER QYYQLFLNLL EAQGYAVVPM ENDVLKVVKS SAAKVEPLP LVGEGSDNYA GDEMVTKVVP VRNVSVRELA PILRQMIDSA GSGNVVNYDP SNVIMLTGRA SVVERLTEVI Q RVDHAGNR TEEVIPLDNA SASEIARVLE SLTKNSGENQ PATLKSQIVA DERTNSVIVS GDPATRDKMR RLIRRLDSEM ER SGNSQVF YLKYSKAEDL VDVLKQVSGT LTAAKEEAEG TVGSGREIVS IAASKHSNAL IVTAPQDIMQ SLQSVIEQLD IRR AQVHVE ALIVEVAEGS NINFGVQWAS KDAGLMQFAN GTQIPIGTLG AAISQAKPQK GSTVISENGA TTINPDTNGD LSTL AQLLS GFSGTAVGVV KGDWMALVQA VKNDSSSNVL STPSITTLDN QEAFFMVGQD VPVLTGSTVG SNNSNPFNTV ERKKV GIML KVTPQINEGN AVQMVIEQEV SKVEGQTSLD VVFGERKLKT TVLANDGELI VLGGLMDDQA GESVAKVPLL GDIPLI GNL FKSTADKKEK RNLMVFIRPT ILRDGMAADG VSQRKYNYMR AEQIYRDEQG LSLMPHTAQP VLPAQNQALP PEVRAFL NA GRTR

UniProtKB: Secretin GspD 2

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Macromolecule #2: Type II secretion system lipoprotein

MacromoleculeName: Type II secretion system lipoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC
Molecular weightTheoretical: 12.18578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CASHNENASL LAKKQAQNIS QNLPIKSAGY TLVLAQSSGT TVKMTIISEA GTQTTQTPDA FLTSYQRQMC ADPTVKLMLT EGINYSITI NDTRTGNQYQ RKLDRTTCGI VKA

UniProtKB: Pilotin AspS 2

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37928
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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