+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21899 | ||||||||||||
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Title | CryoEM structure of human SEMA6A dimer | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cell adhesion involved in sprouting angiogenesis / semaphorin receptor binding / negative regulation of sprouting angiogenesis / 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 / negative chemotaxis ...negative regulation of cell adhesion involved in sprouting angiogenesis / semaphorin receptor binding / negative regulation of sprouting angiogenesis / 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 / negative chemotaxis / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / cytoskeleton organization / negative regulation of angiogenesis / axon guidance / animal organ morphogenesis / negative regulation of ERK1 and ERK2 cascade / nervous system development / cell surface receptor signaling pathway / positive regulation of cell migration / axon / apoptotic process / extracellular space / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_21899.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-21899-v30.xml emd-21899.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_21899.png | 147.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21899 | HTTPS FTP |
-Related 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_21899.map.gz / Format: CCP4 / Size: 4.1 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 : SEMA6A dimer
Entire | Name: SEMA6A dimer |
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Components |
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-Supramolecule #1: SEMA6A dimer
Supramolecule | Name: SEMA6A dimer / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SEMA6A
Macromolecule | Name: SEMA6A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ET GFPEDSE PISISHGNYT KQYPVFVGHK PGRNTTQRHR LDIQM IMIM NGTLYIAARD HIYTVDIDTS HTEEIYCSKK LTWKSRQADV DTCRMKGKHK DECHNF IKV LLKKNDDALF VCGTNAFNPS CRNYKMDTLE PFGDEFSGMA RCPYDAKHAN VALFADG KL ...String: ET GFPEDSE PISISHGNYT KQYPVFVGHK PGRNTTQRHR LDIQM IMIM NGTLYIAARD HIYTVDIDTS HTEEIYCSKK LTWKSRQADV DTCRMKGKHK DECHNF IKV LLKKNDDALF VCGTNAFNPS CRNYKMDTLE PFGDEFSGMA RCPYDAKHAN VALFADG KL YSATVTDFLA IDAVIYRSLG ESPTLRTVKH DSKWLKEPYF VQAVDYGDYI YFFFREIA V EYNTMGKVVF PRVAQVCKND MGGSQRVLEK QWTSFLKARL NCSVPGDSHF YFNILQAVT DVIRINGRDV VLATFSTPYN SIPGSAVCAY DMLDIASVFT GRFKEQKSPD STWTPVPDER VPKPRPGCC AGSSSLERYA TSNEFPDDTL NFIKTHPLMD EAVPSIFNRP WFLRTMVRYR L TKIAVDTA AGPYQNHTVV FLGSEKGIIL KFLARIGNSG FLNDSLFLEE MSVYNSEKCS YD GVEDKRI MGMQLDRASS SLYVAFSTCV IKVPLGRCER YGKCKKTCIA SRDPYCGWIK EGG ACSHLS PNSRLTFEQD IERGNTDGLG DCHN GSWSH PQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: OTHER / Average electron dose: 45.24 e/Å2 / Details: Images were collected with FEI Falcon IV. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: cryoSPARC (ver. 2) |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 281207 |
Details | FEI Falcon IV |
-Atomic model buiding 1
Initial model | PDB ID: |
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