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- PDB-8h8c: Type VI secretion system effector RhsP in its post-autoproteolysi... -

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Basic information

Entry
Database: PDB / ID: 8h8c
TitleType VI secretion system effector RhsP in its post-autoproteolysis and dimeric form
Components
  • C-terminal peptide from Putative Rhs-family protein
  • Putative Rhs-family protein
KeywordsTOXIN / T6SS / Rhs proteins / polymorphic toxins
Function / homology
Function and homology information


WHH domain-containing protein / A nuclease of the HNH/ENDO VII superfamily with conserved WHH / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / : / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core
Similarity search - Domain/homology
Putative Rhs-family protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus serotype O3:K6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsTang, L. / Dong, S.Q. / Rasheed, N. / Wu, H.W. / Zhou, N.K. / Li, H.D. / Wang, M.L. / Zheng, J. / He, J. / Chao, W.C.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC U20A2013 China
National Natural Science Foundation of China (NSFC)32170189 China
CitationJournal: Cell Rep / Year: 2022
Title: Vibrio parahaemolyticus prey targeting requires autoproteolysis-triggered dimerization of the type VI secretion system effector RhsP.
Authors: Le Tang / Shuqi Dong / Nadia Rasheed / Hao Weng Wu / Ningkun Zhou / Huadong Li / Meilin Wang / Jun Zheng / Jun He / William Chong Hang Chao /
Abstract: The rearrangement hotspot (Rhs) repeat is an ancient giant protein fold found in all domains of life. Rhs proteins are polymorphic toxins that could either be deployed as an ABC complex or via a type ...The rearrangement hotspot (Rhs) repeat is an ancient giant protein fold found in all domains of life. Rhs proteins are polymorphic toxins that could either be deployed as an ABC complex or via a type VI secretion system (T6SS) in interbacterial competitions. To explore the mechanism of T6SS-delivered Rhs toxins, we used the gastroenteritis-associated Vibrio parahaemolyticus as a model organism and identified an Rhs toxin-immunity pair, RhsP-RhsP. Our data show that RhsP-dependent prey targeting by V. parahaemolyticus requires T6SS2. RhsP can bind to VgrG2 independently without a chaperone and spontaneously self-cleaves into three fragments. The toxic C-terminal fragment (RhsP) can bind to VgrG2 via a VgrG2-interacting region (VIR). Our electron microscopy (EM) analysis reveals that the VIR is encapsulated inside the Rhs β barrel structure and that autoproteolysis triggers a dramatic conformational change of the VIR. This alternative VIR conformation promotes RhsP dimerization, which significantly contributes to T6SS2-mediated prey targeting by V. parahaemolyticus.
History
DepositionOct 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Putative Rhs-family protein
C: C-terminal peptide from Putative Rhs-family protein
A: Putative Rhs-family protein
D: C-terminal peptide from Putative Rhs-family protein


Theoretical massNumber of molelcules
Total (without water)320,2584
Polymers320,2584
Non-polymers00
Water00
1


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

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Components

#1: Protein Putative Rhs-family protein


Mass: 131985.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In cleaved RhsP, the cleavage at F1131/L1132 allows the VIR to re-position itself in a U-shape manner with both the N and C termini located at the lid region.
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Gene: VP1517 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87PI5
#2: Protein C-terminal peptide from Putative Rhs-family protein


Mass: 28143.795 Da / Num. of mol.: 2 / Mutation: H1354A
Source method: isolated from a genetically manipulated source
Details: Cleaved RhsP in its dimeric form
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Gene: VP1517 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87PI5

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Type VI secretion system effector RhsP in its post-autoproteolysis form
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212763 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00117288
ELECTRON MICROSCOPYf_angle_d0.423388
ELECTRON MICROSCOPYf_dihedral_angle_d26.9072344
ELECTRON MICROSCOPYf_chiral_restr0.042400
ELECTRON MICROSCOPYf_plane_restr0.0023086

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