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- PDB-8gra: Structure of Type VI secretion system cargo delivery vehicle Hcp-... -

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Basic information

Entry
Database: PDB / ID: 8gra
TitleStructure of Type VI secretion system cargo delivery vehicle Hcp-VgrG-PAAR
Components
  • Bacterodales T6SS protein TssD (Hcp)
  • Type VI secretion system spike protein PaarType VI secretion system
  • Type VI secretion system spike protein VgrGType VI secretion system
KeywordsTRANSPORT PROTEIN / Type VI Secretion System / VgrG / Hcp5 / PAAR
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWen, Y. / He, W. / Zhu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072237, 31870132 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
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
J: Type VI secretion system spike protein Paar
B: Bacterodales T6SS protein TssD (Hcp)
I: Type VI secretion system spike protein VgrG
H: Type VI secretion system spike protein VgrG
G: Type VI secretion system spike protein VgrG
A: Bacterodales T6SS protein TssD (Hcp)
F: Bacterodales T6SS protein TssD (Hcp)
E: Bacterodales T6SS protein TssD (Hcp)
D: Bacterodales T6SS protein TssD (Hcp)
C: Bacterodales T6SS protein TssD (Hcp)
J1: Type VI secretion system spike protein Paar
J2: Type VI secretion system spike protein Paar


Theoretical massNumber of molelcules
Total (without water)362,11512
Polymers362,11512
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Type VI secretion system spike protein Paar / Type VI secretion system


Mass: 23725.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: DXA78_05585, F2Z89_01155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E5IG32
#2: Protein
Bacterodales T6SS protein TssD (Hcp) / Type VI secretion system needle protein Hcp / Hcp5


Mass: 14505.281 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: tssD_4, CQW34_01545, DW228_07065, DWW08_15770, EC81_0218805, F2Z25_09975, F2Z89_01225, F9000_04115, FSA06_12535, H3T27_02635, HMPREF0101_00911, HMPREF1018_02079, IB64_010900
Production host: Escherichia coli (E. coli) / References: UniProt: A0A081TQ32
#3: Protein Type VI secretion system spike protein VgrG / Type VI secretion system


Mass: 67969.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: DXA78_05580, F2Z89_01160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E5IG38

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hcp-VgrG-PAAR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacteroides fragilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4300 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354265 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00520708
ELECTRON MICROSCOPYf_angle_d0.60128021
ELECTRON MICROSCOPYf_dihedral_angle_d5.0562784
ELECTRON MICROSCOPYf_chiral_restr0.0523095
ELECTRON MICROSCOPYf_plane_restr0.0053663

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