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- PDB-6aku: Cryo-EM structure of CVA10 empty particle -

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Basic information

Entry
Database: PDB / ID: 6aku
TitleCryo-EM structure of CVA10 empty particle
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / picornavirus uncoating / receptor binding
Function / homology
Function and homology information


picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell ...picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / suppression by virus of host gene expression / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 / AAA+ ATPase domain / Picornavirus 2B protein / RNA-directed RNA polymerase, C-terminal domain / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain ...Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 / AAA+ ATPase domain / Picornavirus 2B protein / RNA-directed RNA polymerase, C-terminal domain / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Poliovirus 3A protein-like / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / Viral coat protein subunit / Helicase, superfamily 3, single-stranded DNA/RNA virus / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Genome polyprotein / Genome polyprotein / VP1
Biological speciesCoxsackievirus A10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhu, L. / Sun, Y. / Fan, J.Y. / Zhu, B. / Cao, L. / Gao, Q. / Zhang, Y.J. / Liu, H.R. / Rao, Z.H. / Wang, X.X.
CitationJournal: Nat Commun / Year: 2018
Title: Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating.
Authors: Ling Zhu / Yao Sun / Jinyan Fan / Bin Zhu / Lei Cao / Qiang Gao / Yanjun Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang /
Abstract: Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, ...Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, utilizing the molecule KREMEN1 as an entry receptor, constitutes a KREMEN1-dependent subgroup within HEV-As. Currently, there is no vaccine or antiviral therapy available for treating diseases caused by CVA10. The atomic-resolution structure of the CVA10 virion, which is within the KREMEN1-dependent subgroup, shows significant conformational differences in the putative receptor binding sites and serotype-specific epitopes, when compared to the SCARB2-dependent subgroup of HEV-A, such as EV71, highlighting specific differences between the sub-groups. We also report two expanded structures of CVA10, an empty particle and uncoating intermediate at atomic resolution, as well as a medium-resolution genome structure reconstructed using a symmetry-mismatch method. Structural comparisons coupled with previous results, reveal an ordered signal transmission process for enterovirus uncoating, converting exo-genetic receptor-attachment inputs into a generic RNA release mechanism.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release

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Structure visualization

Movie
  • 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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)87,2953
Polymers87,2953
Non-polymers00
Water0
1
A: VP1
B: VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,237,719180
Polymers5,237,719180
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: VP1
B: VP2
C: VP3
x 5


  • icosahedral pentamer
  • 436 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)436,47715
Polymers436,47715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
x 6


  • icosahedral 23 hexamer
  • 524 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)523,77218
Polymers523,77218
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 33232.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: W0G0K3
#2: Protein VP2


Mass: 27783.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A0C5AZ80
#3: Protein VP3


Mass: 26279.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A0C5AWF6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Coxsackievirus A10 / Type: VIRUS / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Source (natural)Organism: Coxsackievirus A10
Source (recombinant)Organism: Chlorocebus aethiops (grivet)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Buffer solutionpH: 7.4
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 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: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22725 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0085099
f_angle_d0.736972
f_dihedral_angle_d10.3414014
f_chiral_restr0.048785
f_plane_restr0.006890

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