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- EMDB-6676: CryoEM structure of type II secretion system secretin GspD in Vib... -

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Basic information

Entry
Database: EMDB / ID: EMD-6676
TitleCryoEM structure of type II secretion system secretin GspD in Vibrio cholerae
Map dataVC_GspD post-processing map
Sample
  • Complex: Full length T2SS secretin GspD in Vibrio cholerae
    • Complex: Type II secretion system protein D
      • Protein or peptide: Type II secretion system protein D
KeywordsSecretin / C15 symmetry / T2SS / PROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain ...Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / 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
Similarity search - Domain/homology
Biological speciesVibrio cholerae O1 (bacteria) / Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsYan Z / Yin M
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structural insights into the secretin translocation channel in the type II secretion system.
Authors: Zhaofeng Yan / Meng Yin / Dandan Xu / Yongqun Zhu / Xueming Li /
Abstract: The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. ...The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel. The secretin domain constitutes a novel double β-barrel channel, with at least 60 β-strands in each barrel, and is stabilized by S domains. The outer membrane channel is sealed by β-strand-enriched gates. On the basis of the partially open state captured, we proposed a detailed gate-opening mechanism. Our structures provide a structural basis for understanding the secretin superfamily and the mechanism of substrate translocation in T2SS.
History
DepositionNov 23, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseDec 28, 2016-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wq8
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6676.png

Downloads & links

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Map

FileDownload / File: emd_6676.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVC_GspD post-processing map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 380 pix.
= 501.6 Å		1.32 Å/pix.
x 380 pix.
= 501.6 Å		1.32 Å/pix.
x 380 pix.
= 501.6 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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.12717731 - 0.27107832
Average (Standard dev.)0.00017467806 (±0.00463615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 501.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z501.600501.600501.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.1270.2710.000

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Supplemental data

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Additional map: VC GspD unpost-processing map

Fileemd_6676_additional.map
AnnotationVC_GspD unpost-processing 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 : Full length T2SS secretin GspD in Vibrio cholerae

EntireName: Full length T2SS secretin GspD in Vibrio cholerae
Components
  • Complex: Full length T2SS secretin GspD in Vibrio cholerae
    • Complex: Type II secretion system protein D
      • Protein or peptide: Type II secretion system protein D

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Supramolecule #1: Full length T2SS secretin GspD in Vibrio cholerae

SupramoleculeName: Full length T2SS secretin GspD in Vibrio cholerae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 (bacteria)
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: Type II secretion system protein D

SupramoleculeName: Type II secretion system protein D / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

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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: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961
Molecular weightTheoretical: 70.863078 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: NEFSASFKGT DIQEFINIVG RNLEKTIIVD PSVRGKVDVR SFDTLNEEQY YSFFLSVLEV YGFAVVEMDN GVLKVIKSKD AKTSAIPVL SGEERANGDE VITQVVAVKN VSVRELSPLL RQLIDNAGAG NVVHYDPANI ILITGRAAVV NRLAEIIRRV D QAGDKEIE ...String:
NEFSASFKGT DIQEFINIVG RNLEKTIIVD PSVRGKVDVR SFDTLNEEQY YSFFLSVLEV YGFAVVEMDN GVLKVIKSKD AKTSAIPVL SGEERANGDE VITQVVAVKN VSVRELSPLL RQLIDNAGAG NVVHYDPANI ILITGRAAVV NRLAEIIRRV D QAGDKEIE VVELNNASAA EMVRIVEALN KTTDAQNTPE FLKPKFVADE RTNSILISGD PKVRERLKRL IKQLDVEMAA KG NNRVVYL KYAKAEDLVE VLKGVSENLQ AEKGTGQPTT SKRNEVMIAA HADTNSLVLT APQDIMNAML EVIGQLDIRR AQV LIEALI VEMAEGDGIN LGVQWGSLES GSVIQYGNTG ASIGNVMIGL EEAKDTTQTK AVYDTNNNFL RNETTTTKGD YTKL ASALS SIQGAAVSIA MGDWTALINA VSNDSSSNIL SSPSITVMDN GEASFIVGEE VPVITGSTAG SNNDNPFQTV DRKEV GIKL KVVPQINEGN SVQLNIEQEV SNVLGANGAV DVRFAKRQLN TSVMVQDGQM LVLGGLIDER ALESESKVPL LGDIPL LGQ LFRSTSSQVE KKNLMVFIKP TIIRDGVTAD GITQRKYNYI RAEQLFRAEK GLRLLDDASV PVLPKFGDDR RHSPEIQ AF IEQMEAKQ

UniProtKB: Secretin GspD

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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: 1.6 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 41579
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER

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