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

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Entry
Database: PDB / ID: 6ads
TitleStructure of Seneca Valley Virus in acidic conditions
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Seneca Valley virus
Specimen sourceSeneca 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 2, 2018 / Release: Feb 6, 2019

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9612
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Assembly

Deposited unit
A: VP1
C: VP3
B: VP2
D: VP4


Theoretical massNumber of molelcules
Total (without water)91,2794
Polyers91,2794
Non-polymers00
Water0
1
A: VP1
C: VP3
B: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,476,755240
Polyers5,476,755240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)17760
ΔGint (kcal/M)-103
Surface area (Å2)30580
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
x 5


  • icosahedral pentamer
  • 456 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)456,39620
Polyers456,39620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
C: VP3
B: VP2
D: VP4
x 6


  • icosahedral 23 hexamer
  • 548 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)547,67524
Polyers547,67524
Non-polymers00
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

#1: Protein/peptide VP1


Mass: 28494.023 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus
#2: Protein/peptide VP3


Mass: 25548.059 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus
#3: Protein/peptide VP2


Mass: 29843.289 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus
#4: Protein/peptide VP4


Mass: 7393.875 Da / Num. of mol.: 1 / Source: (natural) Seneca valley virus

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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 / 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: 13010 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0096297
ELECTRON MICROSCOPYf_angle_d0.9758620
ELECTRON MICROSCOPYf_dihedral_angle_d9.7413709
ELECTRON MICROSCOPYf_chiral_restr0.060956
ELECTRON MICROSCOPYf_plane_restr0.0081115

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