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- EMDB-6829: Cryo-EM Structure of CVA6 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6829
TitleCryo-EM Structure of CVA6 VLP
Map data
Sample
  • Virus: Coxsackievirus A6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: capsid protein VP0
KeywordsCoxsackievirus A6 / virus-like particle / cryo-EM / near-atomic resolution structure / epitope / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated activation of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A6
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChen J / Zhang C
CitationJournal: J Virol / Year: 2018
Title: A 3.0-Angstrom Resolution Cryo-Electron Microscopy Structure and Antigenic Sites of Coxsackievirus A6-Like Particles.
Authors: Jinhuan Chen / Chao Zhang / Yu Zhou / Xiang Zhang / Chaoyun Shen / Xiaohua Ye / Wen Jiang / Zhong Huang / Yao Cong /
Abstract: Coxsackievirus A6 (CVA6) has recently emerged as one of the predominant causative agents of hand, foot, and mouth disease (HFMD). The structure of the CVA6 mature viral particle has not been solved ...Coxsackievirus A6 (CVA6) has recently emerged as one of the predominant causative agents of hand, foot, and mouth disease (HFMD). The structure of the CVA6 mature viral particle has not been solved thus far. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 represent a promising CVA6 vaccine candidate. Here, we report the first cryo-electron microscopy (cryo-EM) structure of the CVA6 VLP at 3.0-Å resolution. The CVA6 VLP exhibits the characteristic features of enteroviruses but presents an open channel at the 2-fold axis and an empty, collapsed VP1 pocket, which is broadly similar to the structures of the enterovirus 71 (EV71) VLP and coxsackievirus A16 (CVA16) 135S expanded particle, indicating that the CVA6 VLP is in an expanded conformation. Structural comparisons reveal that two common salt bridges within protomers are maintained in the CVA6 VLP and other viruses of the genus, implying that these salt bridges may play a critical role in enteroviral protomer assembly. However, there are apparent structural differences among the CVA6 VLP, EV71 VLP, and CVA16 135S particle in the surface-exposed loops and C termini of subunit proteins, which are often antigenic sites for enteroviruses. By immunological assays, we identified two CVA6-specific linear B-cell epitopes (designated P42 and P59) located at the GH loop and the C-terminal region of VP1, respectively, in agreement with the structure-based prediction of antigenic sites. Our findings elucidate the structural basis and important antigenic sites of the CVA6 VLP as a strong vaccine candidate and also provide insight into enteroviral protomer assembly. Coxsackievirus A6 (CVA6) is becoming one of the major pathogens causing hand, foot, and mouth disease (HFMD), leading to significant morbidity and mortality in children and adults. However, no vaccine is currently available to prevent CVA6 infection. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 are a promising CVA6 vaccine candidate. Here, we present a 3.0-Å structure of the CVA6 VLP determined by cryo-electron microscopy. The overall architecture of the CVA6 VLP is similar to those of the expanded structures of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), but careful structural comparisons reveal significant differences in the surface-exposed loops and C termini of each capsid protein of these particles. In addition, we identified two CVA6-specific linear B-cell epitopes and mapped them to the GH loop and the C-terminal region of VP1, respectively. Collectively, our findings provide a structural basis and important antigenic information for CVA6 VLP vaccine development.
History
DepositionSep 29, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseOct 25, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5yhq
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5yhq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6829.png

Downloads & links

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Map

FileDownload / File: emd_6829.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-8.361276 - 15.031385999999999
Average (Standard dev.)0.0000016683748 (±0.9999974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-8.36115.0310.000

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Supplemental data

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Sample components

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Entire : Coxsackievirus A6

EntireName: Coxsackievirus A6
Components
  • Virus: Coxsackievirus A6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: capsid protein VP0

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Supramolecule #1: Coxsackievirus A6

SupramoleculeName: Coxsackievirus A6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 86107 / Sci species name: Coxsackievirus A6 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 33.644395 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NDPISNAIEN AVSTLADTTI SRVTAANTAA SSHSLGTGRV PALQAAETGA SSNASDENLI ETRCVMNRNG VNEASVEHFY SRAGLVGVV EVKDSGTSQD GYTVWPIDVM GFVQQRRKLE LSTYMRFDAE FTFVSNLNDS TTPGMLLQYM YVPPGAPKPD G RKSYQWQT ...String:
NDPISNAIEN AVSTLADTTI SRVTAANTAA SSHSLGTGRV PALQAAETGA SSNASDENLI ETRCVMNRNG VNEASVEHFY SRAGLVGVV EVKDSGTSQD GYTVWPIDVM GFVQQRRKLE LSTYMRFDAE FTFVSNLNDS TTPGMLLQYM YVPPGAPKPD G RKSYQWQT ATNPSIFAKL SDPPPQVSVP FMSPASAYQW FYDGYPTFGE HKQATNLQYG QCPNNMMGHF AIRTVSESTT GK NVHVRVY MRIKHVRAWV PRPFRSQAYM VKNYPTYSQT ISNTAADRAS ITTTDYEGGV PANPQRTF

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 26.375834 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GLPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCRIE TILEVNNTTG TTGVNRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP ...String:
GLPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCRIE TILEVNNTTG TTGVNRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP WISNTHFRAV KTGGVYDYYA TGIVTIWYQT NFVVPPDTPS EANIIALGAA QENFTLKLCK DTDEIRQTAE YQ

UniProtKB: Genome polyprotein

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Macromolecule #3: capsid protein VP0

MacromoleculeName: capsid protein VP0 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 35.351426 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGAQVSAQKS GTHETGNIAT EGSTINFTNI NYYKDSYAAS ASRQDFTQDP TKFTSPVLDA IKEAAAPLQS PSVEACGYSD RVAQLTVGN STITTQEAAN IVLSYGEWPG YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDTG V FGQNAQFH ...String:
MGAQVSAQKS GTHETGNIAT EGSTINFTNI NYYKDSYAAS ASRQDFTQDP TKFTSPVLDA IKEAAAPLQS PSVEACGYSD RVAQLTVGN STITTQEAAN IVLSYGEWPG YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDTG V FGQNAQFH YLYRSGFCMH VQCNASKFHQ GALLVVVIPE FVVAASSPAT KPNGQGLYPD FAHTNPGKEG QVFRDPYVLD AG IPLSQAL VFPHQWINLR TNNCATIIMP YVNALPFDSA LNHSNFGLAV IPISPLKYCN GATTEVPITL TIAPLNSEFS GLR QAIKQ

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11596
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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