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Yorodumi- EMDB-13587: Photorhabdus laumondii T6SS-associated Rhs protein carrying the T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13587 | |||||||||
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Title | Photorhabdus laumondii T6SS-associated Rhs protein carrying the Tre23 toxin domain | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RHS / TVISS / T6SS / TOXIN | |||||||||
Function / homology | RHS repeat / RHS Repeat / PAAR motif / PAAR motif / YD repeat / Rhs repeat-associated core / membrane => GO:0016020 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Photorhabdus laumondii (bacteria) / Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Jurenas D / Talachia Rosa L | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Mounting, structure and autocleavage of a type VI secretion-associated Rhs polymorphic toxin. Authors: Dukas Jurėnas / Leonardo Talachia Rosa / Martial Rey / Julia Chamot-Rooke / Rémi Fronzes / Eric Cascales / Abstract: Bacteria have evolved toxins to outcompete other bacteria or to hijack host cell pathways. One broad family of bacterial polymorphic toxins gathers multidomain proteins with a modular organization, ...Bacteria have evolved toxins to outcompete other bacteria or to hijack host cell pathways. One broad family of bacterial polymorphic toxins gathers multidomain proteins with a modular organization, comprising a C-terminal toxin domain fused to a N-terminal domain that adapts to the delivery apparatus. Polymorphic toxins include bacteriocins, contact-dependent growth inhibition systems, and specialized Hcp, VgrG, PAAR or Rhs Type VI secretion (T6SS) components. We recently described and characterized Tre23, a toxin domain fused to a T6SS-associated Rhs protein in Photorhabdus laumondii, Rhs1. Here, we show that Rhs1 forms a complex with the T6SS spike protein VgrG and the EagR chaperone. Using truncation derivatives and cross-linking mass spectrometry, we demonstrate that VgrG-EagR-Rhs1 complex formation requires the VgrG C-terminal β-helix and the Rhs1 N-terminal region. We then report the cryo-electron-microscopy structure of the Rhs1-EagR complex, demonstrating that the Rhs1 central region forms a β-barrel cage-like structure that encapsulates the C-terminal toxin domain, and provide evidence for processing of the Rhs1 protein through aspartyl autoproteolysis. We propose a model for Rhs1 loading on the T6SS, transport and delivery into the target cell. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13587.map.gz | 65.5 MB | EMDB map data format | |
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Header (meta data) | emd-13587-v30.xml emd-13587.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13587_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_13587.png | 49.6 KB | ||
Masks | emd_13587_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-13587.cif.gz | 6.6 KB | ||
Others | emd_13587_half_map_1.map.gz emd_13587_half_map_2.map.gz | 65.5 MB 65.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13587 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13587 | HTTPS FTP |
-Related structure data
Related structure data | 7pq5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13587.map.gz / Format: CCP4 / Size: 83.7 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: 0.93 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13587_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13587_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13587_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tre23
Entire | Name: Tre23 |
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Components |
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-Supramolecule #1: Tre23
Supramolecule | Name: Tre23 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Photorhabdus laumondii (bacteria) |
-Macromolecule #1: Tre23
Macromolecule | Name: Tre23 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) |
Molecular weight | Theoretical: 165.588828 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MSLGDEIVTR IARVGARHAV HVSPPQGSPG PAAAREGDPI KHASFLGALA GAITGALIGA AVFAAASALV GLTILTGGLA TVAVIALGT AATFALGDVI SAASSAVTNM VDSIGPPSGT LTSGSPNVFI EGQPAARATT DIAVCSKHPA PPLIAQGSET V LINGSPAA ...String: MSLGDEIVTR IARVGARHAV HVSPPQGSPG PAAAREGDPI KHASFLGALA GAITGALIGA AVFAAASALV GLTILTGGLA TVAVIALGT AATFALGDVI SAASSAVTNM VDSIGPPSGT LTSGSPNVFI EGQPAARATT DIAVCSKHPA PPLIAQGSET V LINGSPAA RVDDKLACGA TIKSGAKTVF IGSGQGTYLA VADEFSAWER AILIAVEFLV PPSRGALKGL GKLFTKPGQG IQ GVLKGAK AGAKKAKALL SNRISCAKKA FRETEGAKRY REATKKFFTG DPIDVTTGQL FDQRTDITLG QTLPLVFLRS WVP EEQGLL GPGWTDSFSE CALATGDRVE IRTTEGASLY FALPAAYTHS VNPDHPDFTL SRGEQGYILR HRDSPVSKYF TLPH PSSAS KEAPRRWLLT EHRDVYDNRL RFIYNKHCQL TQVLHSDGPE LTLLYNLRGQ LTEIRRTDER LQEVMARYHY HDNGR LAEA DSTQNFHLYY EYNAQGLISR WSDGDQTWVD YRYDKQGRCT DSVGAGGFYP VHLDYAPGIT RSTTPQGHTT TGHYND QQL ITEIHTPCGG VTRYEYDRWG NLVRQILPEG ETLTLTYLAD TGRVTSLTEA TGAVWQYSYE ADSLQLTGMT DPLQRTW LP QYDEQGQPAG FIAPDGRKTT LTRNAFGLVT SETDPDGNSR TQEYDKHQRL VRVLDEENRT VSLGYDSQDR LRSLTAAG A LWRWRYDRHH RVAVSDRPDN QLEHFTHDRH GNLTCWTDAR GVKWQVEYGP FDLPVARRDG EGHRWQYRYD ADTLQLTQV INPQGETYSY TLDADGRVIT EQDYAGTQWH YRYDRSGNCI EKRDGEENVT RYDYDAARRL TTLHTPEGPT RYHYDSVGRL LTVDSPDST LHFEYDGQDR IVREIQPHGE IQRHYPDNRT AERQLLTGET APVTGPARFS GQTHPGRWQS RREVNRVGEL I TLTLAGQA PLTIERDDAG RDTGRYVDGG FILRQQYSLM GQLTAQRAGR NPYFFRPAEP DEIEGPAYAG VARRYEYDTA LN LTAASDD GQQVNYLLNG NGQVISVGEG RTLREHYQYD ETGYPSRRFD GVQEIMGETL YQEGHRLNWV GSHRFVYDRA GRM QEKQFL AEGCRLALTK YRWNSQNQLT GLITPDGIPW EYRYDAFGRR TEKRCIQSGK LTTYLWDGNV PAEIREYQHG RLKM IRHLV FDGWELVAQQ TQAFTLNLDN RVELMAGEVQ TQYAVSAPTG EPLALFDPAG KRVWRRPKQS LYGLRLGGYG ENPQL DPGL RFAGQLFDEE SGLFYNRFRY YLPEATCYLS PDPTGLWGGE NTYRYVQNPT KFINPLGLAG ENVFIHATNK AGFDGI MKS GVLHPNVSGK VAITDVLMSP KDVMRDLLIN NPNHIGRGDY AIIFKIDPGE RGNIRSPSRL EYTHEGKLKL NNILYAG KN PYAILEHLDY DTRLKLTDNQ VKIRKCGGKV DDYKDDDDK UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8.5 Details: 50 mM Tris-HCl pH8.5, 250 mM NaCl, 1 mM TCEP, cOmpleteTM protease inhibitor cocktail (Sigma-Aldrich) |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec. / Pretreatment - Pressure: 25.0 kPa / Details: 2 mAu current |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-37 / Number grids imaged: 1 / Number real images: 8550 / Average exposure time: 3.7 sec. / Average electron dose: 49.75 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 75.76 |
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Output model | PDB-7pq5: |