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- EMDB-6916: CryoEM structure of ETEC Secretin GspD -

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Basic information

Entry
Database: EMDB / ID: EMD-6916
TitleCryoEM structure of ETEC Secretin GspD
Map datasharpening map
Sample
  • Complex: GspD
    • Protein or peptide: GspD
Biological speciesEscherichia coli ETEC H10407 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsYin M / Yan Z / Li X
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-
UpdateJun 20, 2018-
Current statusJun 20, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6916.png

Downloads & links

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Map

FileDownload / File: emd_6916.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.090696 - 0.19875893
Average (Standard dev.)0.0004310904 (±0.0051945006)
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-0.0910.1990.000

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Supplemental data

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Sample components

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Entire : GspD

EntireName: GspD
Components
  • Complex: GspD
    • Protein or peptide: GspD

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Supramolecule #1: GspD

SupramoleculeName: GspD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: outer membrane channel Secretin
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: GspD

MacromoleculeName: GspD / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEATFTANFK DTDLKSFIET VGANLNKTI IMGPGVQGKV SIRTMTPLNE RQYYQLFLNL LEAQGYAVVP MENDVLKVVK S SAAKVEPL PLVGEGSDNY AGDEMVTKVV PVRNVSVREL APILRQMIDS AGSGNVVNYD PS NVIMLTG RASVVERLTE VIQRVDHAGN ...String:
EEATFTANFK DTDLKSFIET VGANLNKTI IMGPGVQGKV SIRTMTPLNE RQYYQLFLNL LEAQGYAVVP MENDVLKVVK S SAAKVEPL PLVGEGSDNY AGDEMVTKVV PVRNVSVREL APILRQMIDS AGSGNVVNYD PS NVIMLTG RASVVERLTE VIQRVDHAGN RTEEVIPLDN ASASEIARVL ESLTKNSGEN QPA TLKSQI VADERTNSVI VSGDPATRDK MRRLIRRLDS EMERSGNSQV FYLKYSKAED LVDV LKQVS GTLTAAKEEA EGTVGSGREI VSIAASKHSN ALIVTAPQDI MQSLQSVIEQ LDIRR AQVH VEALIVEVAE GSNINFGVQW ASKDAGLMQF ANGTQIPIGT LGAAISQAKP QKGSTV ISE NGATTINPDT NGDLSTLAQL LSGFSGTAVG VVKGDWMALV QAVKNDSSSN VLSTPSI TT LDNQEAFFMV GQDVPVLTGS TVGSNNSNPF NTVERKKVGI MLKVTPQINE GNAVQMVI E QEVSKVEGQT SLDVVFGERK LKTTVLANDG ELIVLGGLMD DQAGESVAKV PLLGDIPLI GNLFKSTADK KEKRNLMVFI RPTILRDGMA ADGVSQRKYN YMRAEQIYRD EQGLSLMPHT AQPVLPAQN QALPPEVRAF LNAGRTR

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

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 1.4)
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 17528

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