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- EMDB-34087: The cargo delivery vehicle Hcp-VgrG-PAAR of the Type VI secretion... -

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Basic information

Entry
Database: EMDB / ID: EMD-34087
TitleThe cargo delivery vehicle Hcp-VgrG-PAAR of the Type VI secretion system
Map data
Sample
  • Complex: Hcp-VgrG-PAAR of the Type VI secretion system
KeywordsT6SS GA3 / cargo delivery system / PROTEIN TRANSPORT
Function / homology
Function and homology information


type VI protein secretion system complex / :
Similarity search - Function
Hemolysin coregulated protein (Hcp) TssD / Hemolysin coregulated protein Hcp (TssD) / PAAR motif / PAAR motif / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Bacterodales T6SS protein TssD (Hcp) / Type VI secretion system spike protein Paar / Type VI secretion system spike protein VgrG
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHe W / Wu K / Zhu L / Wen Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31600593 China
CitationJournal: Cell Rep / Year: 2023
Title: Structure and assembly of type VI secretion system cargo delivery vehicle.
Authors: Wenbo He / Ke Wu / Zhenlin Ouyang / Yixin Bai / Wen Luo / Di Wu / Hao An / Yucheng Guo / Min Jiao / Qian Qin / Jiaxin Zhang / Yi Wu / Junjun She / Peter M Hwang / Fang Zheng / Li Zhu / Yurong Wen /
Abstract: Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS ...Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions.
History
DepositionAug 14, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34087.png

Downloads & links

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Map

FileDownload / File: emd_34087.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.3287946 - 0.76523536
Average (Standard dev.)-0.0004510283 (±0.01494133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34087_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_34087_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 : Hcp-VgrG-PAAR of the Type VI secretion system

EntireName: Hcp-VgrG-PAAR of the Type VI secretion system
Components
  • Complex: Hcp-VgrG-PAAR of the Type VI secretion system

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Supramolecule #1: Hcp-VgrG-PAAR of the Type VI secretion system

SupramoleculeName: Hcp-VgrG-PAAR of the Type VI secretion system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides fragilis (bacteria)

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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

Concentration0.07 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.4 sec. / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 10500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 511692
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135343
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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