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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9613 | |||||||||
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Title | Structure of Seneca Valley Virus in neutral condition | |||||||||
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![]() | VIRUS | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
![]() | Lou ZY / Cao L | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 74.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.4 KB 12.4 KB | Display Display | ![]() |
Images | ![]() | 87.9 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6adtMC ![]() 9607C ![]() 9608C ![]() 9611C ![]() 9612C ![]() 6adlC ![]() 6admC ![]() 6adrC ![]() 6adsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.025 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Seneca valley virus
Entire | Name: ![]() |
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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: all / 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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-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: ![]() |
Molecular weight | Theoretical: 28.494023 KDa |
Sequence | String: STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TATGTQQDDG YFCLLTPRPT VASRPATRF GLYVSPSDSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P YHFTGRTP ...String: STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TATGTQQDDG YFCLLTPRPT VASRPATRF GLYVSPSDSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P YHFTGRTP RAFASKGGKV SFVLPWNSVS SVLPVRWGGA SKLSSATRGL PAHADWGTIY AFIPRPNEKK STAVKHVAVY IR YKNARAW CPSMLPFRSY K |
-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: ![]() |
Molecular weight | Theoretical: 26.393938 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 H |
-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: ![]() |
Molecular weight | Theoretical: 29.843289 KDa |
Sequence | String: DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG ...String: DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG TYYRPPNWTW GPNFINPYQV TVFPHQILNA RTSTSVDINV PYIGETPTQS SETQNSWTLL VMVLVPLDYK EG ATTDPEI TFSVRPTSPY FNGLRNRYTT |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.393875 KDa |
Sequence | String: GNVQTTSKND FDSRGNNGNM TFNYYANTYQ NSVDFSTSSS ASGAGPGNSR GGLAGLLTNF SGILNPLGYL K |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11096 |
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-6adt: |