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- EMDB-9612: Structure of Seneca Valley Virus in acidic conditions -

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Basic information

Entry
Database: EMDB / ID: EMD-9612
TitleStructure of Seneca Valley Virus in acidic conditions
Map data
Sample
  • Virus: Seneca valley virus
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4
KeywordsSeneca Valley virus / VIRUS
Biological speciesSeneca valley virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou ZY / Cao L
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: 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
DepositionAug 2, 2018-
Header (metadata) releaseFeb 6, 2019-
Map releaseFeb 6, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ads
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9612.png

Downloads & links

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Map

FileDownload / File: emd_9612.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 550 pix.
= 596.75 Å		1.09 Å/pix.
x 550 pix.
= 596.75 Å		1.09 Å/pix.
x 550 pix.
= 596.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.06695408 - 0.13471457
Average (Standard dev.)0.00078664004 (±0.006633358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 596.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z596.750596.750596.750
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS550550550
D min/max/mean-0.0670.1350.001

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Supplemental data

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Sample components

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Entire : Seneca valley virus

EntireName: Seneca valley virus
Components
  • Virus: Seneca valley virus
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4

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Supramolecule #1: Seneca valley virus

SupramoleculeName: 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

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 28.494023 KDa
SequenceString: 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

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Macromolecule #2: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 25.548059 KDa
SequenceString: GPIPTAPREN SLMFLSTTPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFGRVD AYVPYVAVPT QFDDKPLISF PITLSDPVY QNTLVGAISS NFANYRGCIQ ITLTFCGPMM ARGKFLLSYS PPNGTQPQTL SEAMQCTYSI WDIGLNSSWT F VIPYISPS ...String:
GPIPTAPREN SLMFLSTTPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFGRVD AYVPYVAVPT QFDDKPLISF PITLSDPVY QNTLVGAISS NFANYRGCIQ ITLTFCGPMM ARGKFLLSYS PPNGTQPQTL SEAMQCTYSI WDIGLNSSWT F VIPYISPS DYRETRAITN SVYSADGWFS LHKLTKITLP PDCPQSPCIL FFASAGEDYT LRLPVDCNPS YVF

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 29.843289 KDa
SequenceString: 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

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 7.393875 KDa
SequenceString:
GNVQTTSKND FDSRGNNGNM TFNYYANTYQ NSVDFSTSSS ASGAGPGNSR GGLAGLLTNF SGILNPLGYL K

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.63 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13010
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6ads:
Structure of Seneca Valley Virus in acidic conditions

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