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- EMDB-62181: Cryo-EM structure of the Type II secretion system protein from Vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-62181
TitleCryo-EM structure of the Type II secretion system protein from Vibrio cholerae
Map data
Sample
  • Complex: GspD
    • Protein or peptide: General secretion pathway protein D
KeywordsSecretion / GspD / nanopore sequencing / 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 / 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
General secretion pathway protein D
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsLiu RH / Feng QS / Zhang K / Dai X / Dai J / Guo XR / Lin WF / Wang ZF / Fu Y / Li Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Type II secretion system protein from Vibrio cholerae
Authors: Liu RH / Feng QS / Zhang K / Dai X / Dai J / Guo XR / Lin WF / Wang ZF / Fu Y / Li Y
History
DepositionOct 24, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62181.png

Downloads & links

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Map

FileDownload / File: emd_62181.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-13.517094999999999 - 27.792169999999999
Average (Standard dev.)0.000000000002428 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 320.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62181_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62181_half_map_2.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 : GspD

EntireName: GspD
Components
  • Complex: GspD
    • Protein or peptide: General secretion pathway protein D

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Supramolecule #1: GspD

SupramoleculeName: GspD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: General secretion pathway protein D

MacromoleculeName: General secretion pathway protein D / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.581309 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNNRVVYLK YAKAEDLVEV LKGVSENLQA EKGTGQPTTS KRNEVMIAAH ADTNSLVLTA PQDIMNAMLE VIGQLDIRRA QVLIEALIV EMAEGDGINL GVQWGSLESG SVIQYGNTGA SIGNVMIGLE EAKDTTQTKA VYDTNNNFLR NETTTTKGDY T KLASALSS ...String:
MGNNRVVYLK YAKAEDLVEV LKGVSENLQA EKGTGQPTTS KRNEVMIAAH ADTNSLVLTA PQDIMNAMLE VIGQLDIRRA QVLIEALIV EMAEGDGINL GVQWGSLESG SVIQYGNTGA SIGNVMIGLE EAKDTTQTKA VYDTNNNFLR NETTTTKGDY T KLASALSS IQGAAVSIAM GDWTALINAV SNDSSSNILS SPSITVMDNG EASFIVGEEV PVITGSTAGS NNDNPFQTVD RK EVGIKLK VVPQINEGNS VQLNIEQEVS NVLGANGAVD VRFAKRQLNT SVMVQDGQML VLGGLIDERA LESESKVPLL GDI PLLGQL FRSTSSQVEK KNLMVFIKPT IIRDGVTADG ITQRKYNYIR AEQLFRAEKG LRLLDDASVP VLPKFGDDRR HSPE IQAFI EQMEAKQWSH PQFEK

UniProtKB: General secretion pathway protein D

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111644
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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