[English] 日本語
Yorodumi
- EMDB-34541: Type VI secretion system effector RhsP in its pre-autoproteolysis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34541
TitleType VI secretion system effector RhsP in its pre-autoproteolysis and monomeric formType VI secretion system
Map data
Sample
  • Complex: Type VI secretion system effector RhsP in its pre-autoproteolysis formType VI secretion system
    • Protein or peptide: Putative Rhs-family protein
KeywordsT6SS / Rhs proteins / polymorphic toxins / TOXIN
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 (bacteria) / Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsTang L / Dong SQ / Rasheed N / Wu HW / Zhou NK / Li HD / Wang ML / Zheng J / He J / Chao WCH
Funding support China, 2 items
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, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_34541.png

Downloads & links

-
Map

FileDownload / File: emd_34541.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.09371838 - 0.15697081
Average (Standard dev.)-0.0000006691601 (±0.004213312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions258258258
Spacing258258258
CellA=B=C: 224.46 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34541_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34541_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Type VI secretion system effector RhsP in its pre-autoproteolysis form

EntireName: Type VI secretion system effector RhsP in its pre-autoproteolysis formType VI secretion system
Components
  • Complex: Type VI secretion system effector RhsP in its pre-autoproteolysis formType VI secretion system
    • Protein or peptide: Putative Rhs-family protein

-
Supramolecule #1: Type VI secretion system effector RhsP in its pre-autoproteolysis form

SupramoleculeName: Type VI secretion system effector RhsP in its pre-autoproteolysis form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)

-
Macromolecule #1: Putative Rhs-family protein

MacromoleculeName: Putative Rhs-family protein / type: protein_or_peptide / ID: 1 / Details: Uncleaved RhsP in its monomeric form / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Molecular weightTheoretical: 160.008469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPENLYFQ SMIPQFVIPL TNCLGQSYHF SSQPIPKGEH KKFDSEQSAK AFLDDFVPLR SSRVEELYHL LGQFPPNVP DEELTPELYA PVFAKALVNG SLYVASFPKT KKNATISSEP TPVPKQVKAK SKQNKAHTSS KTQAKNSASA K PLQTGSEC ...String:
MGSSHHHHHH SQDPENLYFQ SMIPQFVIPL TNCLGQSYHF SSQPIPKGEH KKFDSEQSAK AFLDDFVPLR SSRVEELYHL LGQFPPNVP DEELTPELYA PVFAKALVNG SLYVASFPKT KKNATISSEP TPVPKQVKAK SKQNKAHTSS KTQAKNSASA K PLQTGSEC HEKAGDPVSL VTGAEILTLN DVELPNGFVW SRTYRSSKAS RNQGLGYGWR HAFQFELKEV TDEKHNVTSW EF ISDSADE IEFEPVEHGS TSYQVYVGAS CHFLNPNIRI VTLSSGDQYR FELVEDIWLL KQVRNGIFST FQLRYSRNHR LIE VAHNKR PVLECQYDKQ GRLVELLNAK TEQVLTTYIY DEQDDLVGAT NDLGLTERYE YQDQHLIAKR VRPTGFTHYF EWSG EGSSA KCIRNFGDSG IYDYRFHYEG AKSSYSDSLD NEWTFIHDEQ GHLLEKSSPT GRTWQWHYDH LGRKEKAVFP DNSTT QYQY NQQGQLISKL HSSGAQIQYG YDSLGKLVKT VSPDGDLEKA YYNSLGQRVW DIDALGCVTE YEYDKHGQVV KRESED GKK SRWWWDKQQR LVAHEVDGTL LRYSYGATDL VNGIAYPDGC VAQISYDDYG RRTSIRYFND EDKVGYSEEY AYDEFSR VA QIQTPEGVTS YQWGALAQQE AVIFPDGSHI SYEYDQQRNL TKLVRSDGLA FEFWYDSEGL LSGTVGFDGL HSQFKYDS M GRIIRKDVAD RTVLYSYDDA GFLQHIKAGN GKNIVENHFN YTLGGRLTLA SNRHQTLQYQ YSSFGHLTKR IQGQFEIGE EFNRVGQRVS QTLPDKTSFN FSYDTNGRLS EIRFSDDSLP KIEFQYDVMG RLSVTETESF RESKLYDGVG RLVEQQWSGR EKKYIYNAQ NRISSILDNT AGATHYQYDT LGYVTKVSEA GSTSTFESDS FGNPALADSK VMSDRIEAYA GVRYKYDQQG N QVKREGDG TVQKRVFDAL SQLVEVHGDS SISHYEYDAL GRRTKKITQN GITEFLWEGE RLLGERTADG FRWYLYQPET YI PLAVLEN GSIYLYECDQ VGKPERLKDS AGNIVWSASY DVHGFASIDV EEVRNPLRFQ GQYFDQETNL HYNLARYYDP KLG RFIQQD PISIAGGINH YQYAVNPIQW IAPTGFLCEE GLKRLQQMLA EYQAQSDVPQ EVCDQILEAA KESSVGEDGV RSQV KIRKP NGKNNIRYEY DLDHIDCKKN EITFYRHINY SDGSKRKIQY TVGIEGFVDI YDFVNVQKCD AQVYDTKTSK TVGGR KIIN SEFAGKTVTT KGGDVRFDSD GFPDFTPYSK KTVRVIGLTG DMANDVPLAM ARAKITKYDK SKYVWHHHQD GKTMML IPK SVHSVRNGGV AATGGRSVIQ HNLLNPNNKL NYSSPEELV

UniProtKB: Putative Rhs-family protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 738487

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more