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Yorodumi- EMDB-21898: CryoEM structure of the C. sordellii lethal toxin TcsL in complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21898 | ||||||||||||
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Title | CryoEM structure of the C. sordellii lethal toxin TcsL in complex with SEMA6A | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cell adhesion involved in sprouting angiogenesis / negative regulation of sprouting angiogenesis / semaphorin receptor binding / Other semaphorin interactions / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance / positive regulation of neuron migration / chemorepellent activity / neural crest cell migration / host cell cytosol ...negative regulation of cell adhesion involved in sprouting angiogenesis / negative regulation of sprouting angiogenesis / semaphorin receptor binding / Other semaphorin interactions / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance / positive regulation of neuron migration / chemorepellent activity / neural crest cell migration / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / negative chemotaxis / glycosyltransferase activity / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / negative regulation of angiogenesis / cysteine-type peptidase activity / cytoskeleton organization / host cell endosome membrane / axon guidance / animal organ morphogenesis / negative regulation of ERK1 and ERK2 cascade / nervous system development / toxin activity / cell surface receptor signaling pathway / positive regulation of cell migration / axon / apoptotic process / host cell plasma membrane / extracellular space / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Paeniclostridium sordellii (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Kucharska I / Rubinstein JL / Julien JP | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: Cell / Year: 2020 Title: Recognition of Semaphorin Proteins by P. sordellii Lethal Toxin Reveals Principles of Receptor Specificity in Clostridial Toxins. Authors: Hunsang Lee / Greg L Beilhartz / Iga Kucharska / Swetha Raman / Hong Cui / Mandy Hiu Yi Lam / Huazhu Liang / John L Rubinstein / Daniel Schramek / Jean-Philippe Julien / Roman A Melnyk / Mikko Taipale / Abstract: Pathogenic clostridial species secrete potent toxins that induce severe host tissue damage. Paeniclostridium sordellii lethal toxin (TcsL) causes an almost invariably lethal toxic shock syndrome ...Pathogenic clostridial species secrete potent toxins that induce severe host tissue damage. Paeniclostridium sordellii lethal toxin (TcsL) causes an almost invariably lethal toxic shock syndrome associated with gynecological infections. TcsL is 87% similar to C. difficile TcdB, which enters host cells via Frizzled receptors in colon epithelium. However, P. sordellii infections target vascular endothelium, suggesting that TcsL exploits another receptor. Here, using CRISPR/Cas9 screening, we establish semaphorins SEMA6A and SEMA6B as TcsL receptors. We demonstrate that recombinant SEMA6A can protect mice from TcsL-induced edema. A 3.3 Å cryo-EM structure shows that TcsL binds SEMA6A with the same region that in TcdB binds structurally unrelated Frizzled. Remarkably, 15 mutations in this evolutionarily divergent surface are sufficient to switch binding specificity of TcsL to that of TcdB. Our findings establish semaphorins as physiologically relevant receptors for TcsL and reveal the molecular basis for the difference in tissue targeting and disease pathogenesis between highly related toxins. | ||||||||||||
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_21898.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-21898-v30.xml emd-21898.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_21898.png | 48.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21898 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21898 | HTTPS FTP |
-Validation report
Summary document | emd_21898_validation.pdf.gz | 370.1 KB | Display | EMDB validaton report |
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Full document | emd_21898_full_validation.pdf.gz | 369.6 KB | Display | |
Data in XML | emd_21898_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | emd_21898_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21898 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21898 | HTTPS FTP |
-Related structure data
Related structure data | 6wtsMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21898.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of SEMA6A with TcsL
Entire | Name: Complex of SEMA6A with TcsL |
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Components |
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-Supramolecule #1: Complex of SEMA6A with TcsL
Supramolecule | Name: Complex of SEMA6A with TcsL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: SEMA6A
Supramolecule | Name: SEMA6A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: TcsL
Supramolecule | Name: TcsL / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Paeniclostridium sordellii (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: SEMA6A
Macromolecule | Name: SEMA6A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.85741 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ETGFPEDSEP ISISHGNYTK QYPVFVGHKP GRNTTQRHRL DIQMIMIMNG TLYIAARDHI YTVDIDTSHT EEIYCSKKLT WKSRQADVD TCRMKGKHKD ECHNFIKVLL KKNDDALFVC GTNAFNPSCR NYKMDTLEPF GDEFSGMARC PYDAKHANVA L FADGKLYS ...String: ETGFPEDSEP ISISHGNYTK QYPVFVGHKP GRNTTQRHRL DIQMIMIMNG TLYIAARDHI YTVDIDTSHT EEIYCSKKLT WKSRQADVD TCRMKGKHKD ECHNFIKVLL KKNDDALFVC GTNAFNPSCR NYKMDTLEPF GDEFSGMARC PYDAKHANVA L FADGKLYS ATVTDFLAID AVIYRSLGES PTLRTVKHDS KWLKEPYFVQ AVDYGDYIYF FFREIAVEYN TMGKVVFPRV AQ VCKNDMG GSQRVLEKQW TSFLKARLNC SVPGDSHFYF NILQAVTDVI RINGRDVVLA TFSTPYNSIP GSAVCAYDML DIA SVFTGR FKEQKSPDST WTPVPDERVP KPRPGCCAGS SSLERYATSN EFPDDTLNFI KTHPLMDEAV PSIFNRPWFL RTMV RYRLT KIAVDTAAGP YQNHTVVFLG SEKGIILKFL ARIGNSGFLN DSLFLEEMSV YNSEKCSYDG VEDKRIMGMQ LDRAS SSLY VAFSTCVIKV PLGRCERYGK CKKTCIASRD PYCGWIKEGG ACSHLSPNSR LTFEQDIERG NTDGLGDCHN GSWSHP QFE K |
-Macromolecule #2: TcsL
Macromolecule | Name: TcsL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Glycosyltransferases; Hexosyltransferases |
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Source (natural) | Organism: Paeniclostridium sordellii (bacteria) |
Molecular weight | Theoretical: 63.315875 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SAWSHPQFEK ENLYFQGTNV RINLDGNTRS FIVPVITTEQ IRKNLSYSFY GSGGSYSLSL SPYNMNIDLN LVENDTWVID VDNVVKNIT IESDEIQKGE LIENILSKLN IEDNKIVLNN HTINFYGAIN ESNRFISLTF SILEDINIII EIDLVSKSYK I LLSGNCIK ...String: SAWSHPQFEK ENLYFQGTNV RINLDGNTRS FIVPVITTEQ IRKNLSYSFY GSGGSYSLSL SPYNMNIDLN LVENDTWVID VDNVVKNIT IESDEIQKGE LIENILSKLN IEDNKIVLNN HTINFYGAIN ESNRFISLTF SILEDINIII EIDLVSKSYK I LLSGNCIK LIENSSDIQQ KIDHIGFNGE HQKYIPYSYI DNETKYNGFI DYSKKEGLFT AEFSNESIIR NIYMPDSNNL FI YSSKDLK DIRIINKGDV KLLIGNYFKD NMKVSLSFTI EDTNTIKLNG VYLDENGVAQ ILKFMNNAKS ALNTSNSLMN FLE SINIKN IFYNNLDPNI KFILDTNFII SGSNSIGQFE LICDKDKNIQ PYFIKFKIKE TSYTLYAGNR QNLIVEPSYH LDDS GNISS TVINFSQKYL YGIDRYVNKV IITPNLYTDE INITPVYKPN YICPEVIILD ANYINEKINI NINDLSIRYV WDNDG SDLI LIANSEEDNQ PQVKIRFVNV FKSDTAADKL SFNFSDKQDV SVSKIISTFS LAAGSENLYF QGHHHHHH |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: OTHER / Average electron dose: 45.24 e/Å2 / Details: Dataset was collected with FEI Falcon IV. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |