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- PDB-6adm: Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Vi... -

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Basic information

Entry
Database: PDB / ID: 6adm
TitleAnthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions
Components
  • Anthrax toxin receptor 1
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Seneca Valley virus
Function / homologyPeptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / von Willebrand factor, type A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular ...Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / von Willebrand factor, type A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Anthrax toxin receptor / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / von Willebrand factor A-like domain superfamily / RNA helicase / Uptake and function of anthrax toxins / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / VWFA domain profile. / Anthrax receptor extracellular domain / Anthrax receptor C-terminus region / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / von Willebrand factor type A domain / picornavirus capsid protein / Capsid protein VP4 superfamily, Picornavirus / negative regulation of extracellular matrix assembly / reproductive process / icosahedral viral capsid / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / host cell cytoplasmic vesicle membrane / actin cytoskeleton reorganization / collagen binding / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / transmembrane signaling receptor activity / actin filament binding / ion channel activity / protein complex oligomerization / viral RNA genome replication / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / endosome membrane / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / external side of plasma membrane / structural molecule activity / cell surface / RNA binding / membrane / integral component of membrane / ATP binding / plasma membrane / metal ion binding / Genome polyprotein / Anthrax toxin receptor 1
Function and homology information
Specimen sourceHomo sapiens (human)
Seneca valley virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.84 Å resolution
AuthorsLou, Z.Y. / Cao, L.
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 / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2018 / Release: Feb 6, 2019

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Structure visualization

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  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9608
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9096
Polyers111,8855
Non-polymers241
Water0
1
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,714,535360
Polyers6,713,076300
Non-polymers1,45860
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)19810
ΔGint (kcal/M)-112
Surface area (Å2)39160
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules
x 5


  • icosahedral pentamer
  • 560 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)559,54530
Polyers559,42325
Non-polymers1225
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 671 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)671,45336
Polyers671,30830
Non-polymers1466
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

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Protein/peptide , 5 types, 5 molecules ACBDR

#1: Protein/peptide VP1


Mass: 28459.969 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#2: Protein/peptide VP3


Mass: 26296.883 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#3: Protein/peptide VP2


Mass: 29813.266 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#4: Protein/peptide VP4


Mass: 5998.467 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#5: Protein/peptide Anthrax toxin receptor 1 / Tumor endothelial marker 8


Mass: 21316.020 Da / Num. of mol.: 1 / Mutation: C177A / Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H6X2

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Seneca valley virusSenecavirus / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5 / Source: NATURAL
Source (natural)Organism: Seneca valley virus
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.63 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9167 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097968
ELECTRON MICROSCOPYf_angle_d0.95410873
ELECTRON MICROSCOPYf_dihedral_angle_d10.2754703
ELECTRON MICROSCOPYf_chiral_restr0.0561191
ELECTRON MICROSCOPYf_plane_restr0.0081414

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