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- PDB-5xs4: Structure of Coxsackievirus A6 (CVA6) virus A-particle -

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Basic information

Entry
Database: PDB / ID: 5xs4
TitleStructure of Coxsackievirus A6 (CVA6) virus A-particle
Components(Genome polyprotein) x 3
KeywordsVIRUS / Coxsackievirus A6 / A-particle / icosahedral
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 / 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 coat protein VP4 / Poliovirus 3A protein-like / Peptidase C3A/C3B, picornaviral / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded DNA/RNA virus / AAA+ ATPase domain / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus capsid ...Picornavirus coat protein VP4 / Poliovirus 3A protein-like / Peptidase C3A/C3B, picornaviral / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded DNA/RNA virus / AAA+ ATPase domain / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus capsid / Protein of unknown function DUF3724, picornavirus / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / Protein of unknown function (DUF3724) / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Genome polyprotein
Biological speciesCoxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZheng, Q.B. / He, M.Z. / Xu, L.F. / Yu, H. / Li, S.W. / Cheng, T.
Funding support China, United States, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670933 China
National Natural Science Foundation of China81401669 China
National Science and Technology Major Projects for Major New Drugs Innovation and Development2017ZX09101005-005-003 China
National Science and Technology Major Project of Infectious Diseases2017ZX10304402-002-003 China
Natural Science Foundation of Fujian Province2015J05073 China
National Institutes of HealthR37-GM33050 United States
CitationJournal: Nat Commun / Year: 2017
Title: Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.
Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng ...Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng Hou / Wei Wang / Xiangzhong Ye / Jun Zhang / Timothy S Baker / Tong Cheng / Z Hong Zhou / Xiaodong Yan / Ningshao Xia /
Abstract: Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the ...Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses. Our near-atomic resolution structure of CVA6 A-particle complexed with a neutralizing antibody maps an immune-dominant neutralizing epitope to the surface loops of VP1. The structure-guided cell-based inhibition studies further demonstrate that these loops could serve as excellent targets for designing anti-CVA6 vaccines.Coxsackievirus A6 (CVA6) causes hand, foot and mouth disease in children. Here the authors present the CVA6 procapsid and A-particle cryo-EM structures and identify an immune-dominant neutralizing epitope, which can be exploited for vaccine development.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: 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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Structure viewerMolecule:
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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)87,8383
Polymers87,8383
Non-polymers00
Water0
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)5,270,260180
Polymers5,270,260180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area11070 Å2
ΔGint-72 kcal/mol
Surface area26970 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 5


  • icosahedral pentamer
  • 439 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)439,18815
Polymers439,18815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 527 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)527,02618
Polymers527,02618
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
6
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


  • crystal asymmetric unit, crystal frame
  • 5.27 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,270,260180
Polymers5,270,260180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, -0.80901699, -0.30901699), (0.809017, 0.30901699, 0.5), (-0.30901699, -0.5, 0.809017)373.80562, -142.35019, 231.02458
3generate(-0.30901699, -0.5, -0.809017), (0.5, -0.809017, 0.309017), (-0.80901699, -0.309017, 0.5)604.48163, 231.58858, 373.59019
4generate(-0.309017, 0.5, -0.809017), (-0.5, -0.80901699, -0.309017), (-0.809017, 0.30901699, 0.5)373.24162, 605.04563, 230.67601
5generate(0.5, 0.80901699, -0.309017), (-0.80901699, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699)-0.34857, 461.91601, -0.21543
6generate(-0.80901699, 0.309017, -0.50000001), (0.30901699, -0.5, -0.80901699), (-0.49999999, -0.809017, 0.30901699)461.91602, 461.56744, 461.70059
7generate(1), (-1), (-1)461.35201, 461.35202
8generate(0.809017, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699)-142.35018, 230.32743, 87.5464
9generate(0.5, -0.809017, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.309017, 0.5, 0.80901699)231.58858, 87.76182, -143.12961
10generate(-0.5, -0.80901699, -0.309017), (0.80901699, -0.309017, -0.5), (0.309017, -0.5, 0.80901699)605.04563, 230.67601, 88.11039
11generate(-0.5, -0.80901699, -0.30901699), (-0.809017, 0.30901699, 0.49999999), (-0.309017, 0.50000001, -0.80901699)605.04563, 231.80401, 372.11362
12generate(-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699), (0.5, 0.809017, -0.30901699)461.91602, 0.91257, -1.47657
13generate(1), (1), (1)1.128, -1.128
14generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.809017), (0.5, -0.809017, -0.30901699)-142.35018, 232.15258, 372.67762
15generate(0.5, -0.80901699, 0.309017), (-0.80901699, -0.309017, 0.5), (-0.309017, -0.5, -0.80901699)231.58858, 374.71819, 603.35363
16generate(0.30901699, 0.49999999, 0.809017), (0.50000001, -0.80901699, 0.309017), (0.80901699, 0.30901699, -0.5)-142.00161, 231.58857, 86.63382
17generate(0.30901699, -0.5, 0.809017), (-0.5, -0.80901699, -0.30901699), (0.80901699, -0.309017, -0.5)89.23839, 605.04562, 229.54801
18generate(-0.5, -0.80901699, 0.309017), (-0.809017, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699)462.82858, 461.91602, 460.43944
19generate(-1), (1), (-1)462.48002, 460.22401
20generate(-0.5, 0.80901699, 0.309017), (0.80901699, 0.309017, 0.5), (0.309017, 0.5, -0.80901699)88.6744, -142.35019, 229.19944
21generate(-0.49999999, -0.809017, 0.30901699), (0.80901699, -0.309017, 0.50000001), (-0.30901699, 0.5, 0.80901699)462.82859, 0.564, -0.21543
22generate(-1), (-1), (1)462.48002, 462.48001
23generate(-0.5, 0.809017, 0.30901699), (-0.809017, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699)88.6744, 604.8302, 231.02458
24generate(0.309017, 0.5, 0.80901699), (-0.5, 0.809017, -0.30901699), (-0.80901699, -0.30901699, 0.5)-142.00161, 230.89144, 373.59019
25generate(0.309017, -0.5, 0.80901699), (0.5, 0.80901699, 0.309017), (-0.80901699, 0.309017, 0.5)89.23839, -142.56561, 230.67601
26generate(1), (-1), (-1)1.128, 462.48001, 461.35201
27generate(-0.30901699, -0.5, 0.809017), (-0.5, 0.80901699, 0.30901699), (-0.809017, -0.30901699, -0.5)232.15258, 88.6744, 603.7022
28generate(-0.80901699, -0.309017, 0.5), (0.30901699, 0.5, 0.809017), (-0.5, 0.809017, -0.309017)374.71819, -142.00161, 229.76344
29generate(-0.809017, 0.30901699, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.80901699, 0.309017)231.80401, 89.23839, -143.69361
30generate(-0.309017, 0.5, 0.80901699), (-0.5, -0.80901699, 0.309017), (0.80901699, -0.309017, 0.5)0.91257, 462.82858, -0.564
31generate(0.80901699, 0.30901699, -0.5), (-0.30901699, -0.49999999, -0.809017), (-0.50000001, 0.80901699, -0.309017)87.76182, 604.48163, 229.76344
32generate(0.80901699, -0.309017, -0.5), (-0.30901699, 0.5, -0.809017), (0.5, 0.80901699, 0.30901699)230.67601, 373.24162, -143.69361
33generate(0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017), (0.809017, -0.30901699, 0.5)461.56744, -0.34857, -0.564
34generate(-1), (1), (-1)461.35201, 461.35201
35generate(0.309017, 0.5, -0.80901699), (0.5, -0.80901699, -0.309017), (-0.80901699, -0.309017, -0.5)230.32744, 373.80562, 603.7022
36generate(-0.309017, 0.50000001, -0.80901699), (0.5, 0.80901699, 0.30901699), (0.809017, -0.30901699, -0.49999999)373.24162, -142.56561, 229.54801
37generate(0.5, 0.809017, -0.30901699), (0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.80901699)-0.34857, 0.564, 460.43944
38generate(1), (-1), (-1)462.48001, 460.22402
39generate(0.5, -0.809017, -0.30901699), (-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.809017)373.80562, 604.8302, 229.19944
40generate(-0.309017, -0.5, -0.80901699), (-0.5, 0.80901699, -0.309017), (0.80901699, 0.309017, -0.5)604.48163, 230.89144, 86.63382
41generate(-0.50000001, 0.80901699, -0.309017), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.49999999, 0.809017)230.89144, 374.71819, -143.12961
42generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.309017, 0.5), (0.30901699, -0.5, 0.809017)-142.56561, 231.80401, 88.11039
43generate(0.809017, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.309017)0.564, 0.91257, 461.70058
44generate(-1), (1), (-1)462.48001, 1.128, 461.35202
45generate(-0.80901699, -0.309017, -0.5), (-0.309017, -0.5, 0.80901699), (-0.5, 0.80901699, 0.309017)604.8302, 232.15258, 87.5464
46generate(0.809017, -0.30901699, -0.49999999), (0.309017, -0.50000001, 0.80901699), (-0.5, -0.80901699, -0.30901699)230.67601, 89.23839, 603.91763
47generate(0.309017, -0.5, -0.80901699), (-0.5, -0.809017, 0.30901699), (-0.809017, 0.309017, -0.5)461.56744, 462.82858, 460.78802
48generate(-1), (-1), (1)461.35202, 462.48002, -1.128
49generate(0.30901699, 0.5, -0.809017), (-0.5, 0.809017, 0.30901699), (0.80901699, 0.30901699, 0.5)230.32744, 88.6744, -143.47818
50generate(0.80901699, 0.309017, -0.5), (0.309017, 0.5, 0.80901699), (0.5, -0.80901699, 0.309017)87.76182, -142.00161, 230.46058
51generate(-0.30901699, 0.5, 0.80901699), (0.49999999, 0.809017, -0.30901699), (-0.80901699, 0.309017, -0.50000001)0.91257, -0.34857, 460.78802
52generate(1), (1), (1)1.128, -1.128
53generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.809017, -0.30901699), (0.809017, 0.30901699, 0.5)232.15258, 373.80562, -143.47818
54generate(-0.80901699, -0.30901699, 0.5), (-0.309017, -0.5, -0.80901699), (0.5, -0.809017, 0.30901699)374.71819, 604.48163, 230.46058
55generate(-0.80901699, 0.309017, 0.5), (-0.309017, 0.5, -0.80901699), (-0.5, -0.80901699, -0.309017)231.80401, 373.24162, 603.91763
56generate(-1), (-1), (1)462.48001, 461.35201, -1.128
57generate(-0.809017, -0.30901699, -0.5), (0.30901699, 0.5, -0.809017), (0.5, -0.80901699, -0.30901699)604.8302, 230.32744, 372.67762
58generate(-0.5, 0.809017, -0.309017), (0.80901699, 0.309017, -0.5), (-0.30901699, -0.5, -0.809017)230.89144, 87.76182, 603.35363
59generate(0.5, 0.80901699, 0.309017), (0.809017, -0.30901699, -0.5), (-0.309017, 0.5, -0.809017)-142.56561, 230.676, 372.11362
60generate(0.80901699, -0.309017, 0.5), (0.309017, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017)0.564, 461.56744, -1.47657

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Components

#1: Protein Genome polyprotein


Mass: 33467.273 Da / Num. of mol.: 1 / Fragment: UNP residues 566-870 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, human / Tissue: muscle / References: UniProt: A0A0K2BNC7
#2: Protein Genome polyprotein


Mass: 28095.559 Da / Num. of mol.: 1 / Fragment: UNP residues 7-=325 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: homo sapiens, human / Tissue: muscle / References: UniProt: A0A0K2BNC7
#3: Protein Genome polyprotein


Mass: 26274.836 Da / Num. of mol.: 1 / Fragment: UNP residues 326-565 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: homo sapiens, human / Tissue: muscle / References: UniProt: A0A0K2BNC7

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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 A6 / Type: VIRUS / Entity ID: 1, 2, 3
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus A6
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Coxsackievirus A6 A-particle capsid / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Details: NaCl 137mmol/L, KCl 2.7mmol/L, Na2HPO4 10mmol/L, KH2PO4 2mmol/L
Buffer componentConc.: 20 mmol/L / Name: PBS
SpecimenConc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: 3?L of virus sample was applied and blot for 6 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4300 nm / Cs: 2.3 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 203
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
2EPU1.4.3image acquisition
4CTFFind4.1CTF correction
7Chimeramodel fitting
9Relion1.4initial Euler assignment
10Relion1.4final Euler assignment
11Relion1.4classification
12Relion1.43D reconstruction
13Cootmodel refinement
14Phenixmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 13545
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7152 / Symmetry type: POINT
Atomic model buildingB value: 163.92 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0095044
ELECTRON MICROSCOPYf_angle_d0.9426896
ELECTRON MICROSCOPYf_dihedral_angle_d7.6013993
ELECTRON MICROSCOPYf_chiral_restr0.06771
ELECTRON MICROSCOPYf_plane_restr0.007882

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