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- PDB-5yhq: Cryo-EM Structure of CVA6 VLP -

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Basic information

Entry
Database: PDB / ID: 5yhq
TitleCryo-EM Structure of CVA6 VLP
DescriptorCapsid protein VP1
capsid protein VP3
capsid protein VP0
KeywordsVIRUS LIKE PARTICLE / Coxsackievirus A6 / virus-like particle / cryo-EM / near-atomic resolution structure / epitope
Specimen sourceCoxsackievirus A6 / virus
MethodElectron microscopy (3 Å resolution / Particle / Single particle)
AuthorsChen, J. / Zhang, C. / Huang, Z. / Cong, Y.
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
A 3.0-Angstrom Resolution Cryo-Electron Microscopy Structure and Antigenic Sites of Coxsackievirus A6-Like Particles.
Jinhuan Chen / Chao Zhang / Yu Zhou / Xiang Zhang / Chaoyun Shen / Xiaohua Ye / Wen Jiang / Zhong Huang / Yao Cong

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDerived calculationspdbx_struct_oper_list_pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3]

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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-6829
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Assembly

Deposited unit
A: Capsid protein VP1
C: Capsid protein VP3
B: capsid protein VP0


Theoretical massNumber of molelcules
Total (without water)95,3723
Polyers95,3723
Non-polymers00
Water0
#1
A: Capsid protein VP1
C: Capsid protein VP3
B: capsid protein VP0
x 60


Theoretical massNumber of molelcules
Total (without water)5,722,299180
Polyers5,722,299180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: Capsid protein VP1
C: Capsid protein VP3
B: capsid protein VP0
x 5


  • icosahedral pentamer
  • 477 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)476,85815
Polyers476,85815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Capsid protein VP1
C: Capsid protein VP3
B: capsid protein VP0
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)572,23018
Polyers572,23018
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: Polypeptide(L)Capsid protein VP1


Mass: 33644.395 Da / Num. of mol.: 1 / Source: (gene. exp.) Coxsackievirus A6 / virus / References: UniProt: Q9YLP0
#2: Polypeptide(L)Capsid protein VP3


Mass: 26375.834 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 326-565 / Source: (gene. exp.) Coxsackievirus A6 / virus / References: UniProt: Q6JKS2
#3: Polypeptide(L)capsid protein VP0


Mass: 35351.426 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-325 / Source: (gene. exp.) Coxsackievirus A6 / virus / References: UniProt: Q6JKS2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Coxsackievirus A6 / Type: VIRUS / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Source (natural)Organism: Coxsackievirus A6
Source (recombinant)Organism: Spodoptera frugiperda
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11596 / Symmetry type: POINT
Least-squares processHighest resolution: 3 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0095490
ELECTRON MICROSCOPYf_angle_d0.8217505
ELECTRON MICROSCOPYf_dihedral_angle_d11.6774343
ELECTRON MICROSCOPYf_chiral_restr0.056830
ELECTRON MICROSCOPYf_plane_restr0.007972

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