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Yorodumi- EMDB-9607: Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley V... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9607 | |||||||||
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Title | Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information reproductive process / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / RNA-protein covalent cross-linking / : / : / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction ...reproductive process / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / RNA-protein covalent cross-linking / : / : / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / blood vessel development / lamellipodium membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Uptake and function of anthrax toxins / collagen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / substrate adhesion-dependent cell spreading / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / transmembrane signaling receptor activity / actin filament binding / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / actin cytoskeleton organization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / entry receptor-mediated virion attachment to host cell / RNA helicase activity / endosome membrane / RNA helicase / symbiont entry into host cell / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Senecavirus A / Homo sapiens (human) / Seneca valley virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Lou ZY / Cao L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1. Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li ...Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao / Abstract: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here we determine atomic structures of mature SVV particles alone and in complex with ANTXR1 in both neutral and acidic conditions, as well as empty "spent" particles in complex with ANTXR1 in acidic conditions by cryoelectron microscopy. SVV engages ANTXR1 mainly by the VP2 DF and VP1 CD loops, leading to structural changes in the VP1 GH loop and VP3 GH loop, which attenuate interprotomer interactions and destabilize the capsid assembly. Despite lying on the edge of the attachment site, VP2 D146 interacts with the metal ion in ANTXR1 and is required for cell entry. Though the individual substitution of most interacting residues abolishes receptor binding and virus propagation, a serine-to-alanine mutation at VP2 S177 significantly increases SVV proliferation. Acidification of the SVV-ANTXR1 complex results in a major reconfiguration of the pentameric capsid assemblies, which rotate ∼20° around the icosahedral fivefold axes to form a previously uncharacterized spent particle resembling a potential uncoating intermediate with remarkable perforations at both two- and threefold axes. These structures provide high-resolution snapshots of SVV entry, highlighting opportunities for anticancer therapeutic optimization. | |||||||||
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_9607.map.gz | 66.2 MB | EMDB map data format | |
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Header (meta data) | emd-9607-v30.xml emd-9607.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_9607.png | 250.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9607 | HTTPS FTP |
-Related structure data
Related structure data | 6adlMUC 9608C 9611C 9612C 9613C 6admC 6adrC 6adsC 6adtC M: atomic model generated by this map U: unfit; in different coordinate system*YM C: citing same article (ref.) |
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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_9607.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1 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 : Seneca valley virus
Entire | Name: Seneca valley virus |
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Components |
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-Supramolecule #1: Seneca valley virus
Supramolecule | Name: Seneca valley virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 390157 / Sci species name: Seneca valley virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Senecavirus A |
Molecular weight | Theoretical: 25.785305 KDa |
Sequence | String: NHTNVKFLFD RSRLLNVIKV LEKDAVFPRP FPTATGTQQD DGYFCLLTPR PTVASRPATR FGLYVSPSDS GVLANTSLDF NFYSLACFT YFRSDLEVTV VSLEPDLEFA VGWFPSGSEY QASSFVYDQL HVPYHFTGRT PRAFASKGGK VSFVLPWNSV S SVLPVRWG ...String: NHTNVKFLFD RSRLLNVIKV LEKDAVFPRP FPTATGTQQD DGYFCLLTPR PTVASRPATR FGLYVSPSDS GVLANTSLDF NFYSLACFT YFRSDLEVTV VSLEPDLEFA VGWFPSGSEY QASSFVYDQL HVPYHFTGRT PRAFASKGGK VSFVLPWNSV S SVLPVRWG GASKLSSATR GLPAHADWGT IYAFIPRPNE KKSTAVKHVA VYIRYKNARA WCPSMLPFRS YK |
-Macromolecule #2: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Senecavirus A |
Molecular weight | Theoretical: 26.255791 KDa |
Sequence | String: GPIPTAPREN SLMFLSTTPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFGRVP EPEPASDAYV PYVAVPTQFD DKPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV ...String: GPIPTAPREN SLMFLSTTPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFGRVP EPEPASDAYV PYVAVPTQFD DKPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV IPYISPSDYR ETRAITNSVY SADGWFSLHK LTKITLPPDC PQSPCILFFA SAGEDYTLRL PVDCNPSYVF |
-Macromolecule #3: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Senecavirus A |
Molecular weight | Theoretical: 27.724059 KDa |
Sequence | String: VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGAF TATLHRHFLM KCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG KNMPFQSLGT YYRPPNWTWG P NFINPYQV ...String: VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGAF TATLHRHFLM KCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG KNMPFQSLGT YYRPPNWTWG P NFINPYQV TVFPHQILNA RTSTSVDINV PYIGETPTQS SETQNSWTLL VMVLVPLDYK EGATTDPEIT FSVRPTSPYF NG LRNRYT |
-Macromolecule #4: Anthrax toxin receptor 1
Macromolecule | Name: Anthrax toxin receptor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.31602 KDa |
Recombinant expression | Organism: Enterobacteria phage L1 (virus) |
Sequence | String: SMACYGGFDL YFILDKSGSV LHHWNEIYYF VEQLAHKFIS PQLRMSFIVF STRGTTLMKL TEDREQIRQG LEELQKVLPG GDTYMHEGF ERASEQIYYE NRQGYRTASV IIALTDGELH EDLFFYSERE ANRSRDLGAI VYAVGVKDFN ETQLARIADS K DHVFPVND GFQALQGIIH SILKKSC |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.63 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3171 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6adl: |