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- EMDB-29702: In situ structure of GspD-alpha on the bacterial inner membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-29702
TitleIn situ structure of GspD-alpha on the bacterial inner membrane
Map data
Sample
  • Complex: The GspD-alpha secretin
Keywordschannel / bacterial membrane envelope / MEMBRANE PROTEIN
Biological speciesEscherichia coli K-12 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.0 Å
AuthorsYu Z / Chen M / Ludtke SJ / Wang Z
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143380 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL162842 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190602 United States
CitationJournal: Nat Commun / Year: 2023
Title: Membrane translocation process revealed by in situ structures of type II secretion system secretins.
Authors: Zhili Yu / Yaoming Wu / Muyuan Chen / Tong Huo / Wei Zheng / Steven J Ludtke / Xiaodong Shi / Zhao Wang /
Abstract: The GspD secretin is the outer membrane channel of the bacterial type II secretion system (T2SS) which secrets diverse toxins that cause severe diseases such as diarrhea and cholera. GspD needs to ...The GspD secretin is the outer membrane channel of the bacterial type II secretion system (T2SS) which secrets diverse toxins that cause severe diseases such as diarrhea and cholera. GspD needs to translocate from the inner to the outer membrane to exert its function, and this process is an essential step for T2SS to assemble. Here, we investigate two types of secretins discovered so far in Escherichia coli, GspD, and GspD. By electron cryotomography subtomogram averaging, we determine in situ structures of key intermediate states of GspD and GspD in the translocation process, with resolution ranging from 9 Å to 19 Å. In our results, GspD and GspD present entirely different membrane interaction patterns and ways of transitioning the peptidoglycan layer. From this, we hypothesize two distinct models for the membrane translocation of GspD and GspD, providing a comprehensive perspective on the inner to outer membrane biogenesis of T2SS secretins.
History
DepositionFeb 8, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29702.png

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Map

FileDownload / File: emd_29702.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.76 Å
Density
Contour LevelBy AUTHOR: 0.64
Minimum - Maximum-1.8352609 - 2.0465465
Average (Standard dev.)0.01494649 (±0.14154278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29702_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29702_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The GspD-alpha secretin

EntireName: The GspD-alpha secretin
Components
  • Complex: The GspD-alpha secretin

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Supramolecule #1: The GspD-alpha secretin

SupramoleculeName: The GspD-alpha secretin / type: complex / ID: 1 / Parent: 0
Details: The secretin of bacterial type II secretion system.
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 5.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 250 / Number images used: 32915
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 32915
FSC plot (resolution estimation)

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