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Yorodumi- EMDB-34540: Type VI secretion system effector RhsP in its post-autoproteolysi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34540 | |||||||||
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Title | Type VI secretion system effector RhsP in its post-autoproteolysis and monomeric form | |||||||||
Map data | ||||||||||
Sample |
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Keywords | T6SS / 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 | |||||||||
Biological species | Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Tang L / Dong SQ / Rasheed N / Wu HW / Zhou NK / Li HD / Wang ML / Zheng J / He J / Chao WCH | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34540.map.gz | 42.2 MB | EMDB map data format | |
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Header (meta data) | emd-34540-v30.xml emd-34540.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_34540.png | 90.9 KB | ||
Filedesc metadata | emd-34540.cif.gz | 6.3 KB | ||
Others | emd_34540_half_map_1.map.gz emd_34540_half_map_2.map.gz | 42.1 MB 42.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34540 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34540 | HTTPS FTP |
-Validation report
Summary document | emd_34540_validation.pdf.gz | 726 KB | Display | EMDB validaton report |
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Full document | emd_34540_full_validation.pdf.gz | 725.6 KB | Display | |
Data in XML | emd_34540_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_34540_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34540 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34540 | HTTPS FTP |
-Related structure data
Related structure data | 8h8aMC 8h8bC 8h8cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34540.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34540_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34540_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type VI secretion system effector RhsP in its post-autoproteolysi...
Entire | Name: Type VI secretion system effector RhsP in its post-autoproteolysis form |
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Components |
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-Supramolecule #1: Type VI secretion system effector RhsP in its post-autoproteolysi...
Supramolecule | Name: Type VI secretion system effector RhsP in its post-autoproteolysis form type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) |
-Macromolecule #1: Putative Rhs-family protein
Macromolecule | Name: Putative Rhs-family protein / type: protein_or_peptide / ID: 1 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. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) |
Molecular weight | Theoretical: 131.985109 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 VTGEEILTLN 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 IDPTGF UniProtKB: Putative Rhs-family protein |
-Macromolecule #2: C-terminal peptide from Putative Rhs-family protein
Macromolecule | Name: C-terminal peptide from Putative Rhs-family protein / type: protein_or_peptide / ID: 2 / Details: Cleaved RhsP in its monomeric form / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) |
Molecular weight | Theoretical: 28.143795 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: LCEEGLKRLQ QMLAEYQAQS DVPQEVCDQI LEAAKESSVG EDGVRSQVKI RKPNGKNNIR YEYDLDHIDC KKNEITFYRH INYSDGSKR KIQYTVGIEG FVDIYDFVNV QKCDAQVYDT KTSKTVGGRK IINSEFAGKT VTTKGGDVRF DSDGFPDFTP Y SKKTVRVI ...String: LCEEGLKRLQ QMLAEYQAQS DVPQEVCDQI LEAAKESSVG EDGVRSQVKI RKPNGKNNIR YEYDLDHIDC KKNEITFYRH INYSDGSKR KIQYTVGIEG FVDIYDFVNV QKCDAQVYDT KTSKTVGGRK IINSEFAGKT VTTKGGDVRF DSDGFPDFTP Y SKKTVRVI GLTGDMANDV PLAMARAKIT KYDKSKYVWH HHQDGKTMML IPKSVHSVRN GGVAATGGRS VIQHNLLNPN NK LNYSSPE ELV UniProtKB: Putative Rhs-family protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 368563 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |