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- EMDB-10256: Structure of Coxsackievirus A10 A-particle -

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Basic information

Entry
Database: EMDB / ID: EMD-10256
TitleStructure of Coxsackievirus A10 A-particle
Map data
Sample
  • Virus: Coxsackievirus A10
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
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 / : ...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 / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
Biological speciesCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhao Y / Zhou D / Ni T / Karia D / Kotecha A / Wang X / Rao Z / Jones EY / Fry EE / Ren J / Stuart DI
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10.
Authors: Yuguang Zhao / Daming Zhou / Tao Ni / Dimple Karia / Abhay Kotecha / Xiangxi Wang / Zihe Rao / E Yvonne Jones / Elizabeth E Fry / Jingshan Ren / David I Stuart /
Abstract: Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry ...Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry receptor for the largest receptor-group of hand-foot-and-mouth disease causing viruses, which includes CV-A10. We report here structures of CV-A10 mature virus alone and in complex with KRM1 as well as of the CV-A10 A-particle. The receptor spans the viral canyon with a large footprint on the virus surface. The footprint has some overlap with that seen for the neonatal Fc receptor complexed with enterovirus E6 but is larger and distinct from that of another enterovirus receptor SCARB2. Reduced occupancy of a particle-stabilising pocket factor in the complexed virus and the presence of both unbound and expanded virus particles suggests receptor binding initiates a cascade of conformational changes that produces expanded particles primed for viral uncoating.
History
DepositionAug 23, 2019-
Header (metadata) releaseSep 4, 2019-
Map releaseJan 15, 2020-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6snb
  • Surface level: 0.04
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6snb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10256.png

Downloads & links

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Map

FileDownload / File: emd_10256.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.054125316 - 0.12603869
Average (Standard dev.)0.0013008694 (±0.007235234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0540.1260.001

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Supplemental data

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Sample components

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Entire : Coxsackievirus A10

EntireName: Coxsackievirus A10
Components
  • Virus: Coxsackievirus A10
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Coxsackievirus A10

SupramoleculeName: Coxsackievirus A10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Sci species strain: Kowalik / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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 / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 33.191422 KDa
SequenceString: GDPVEDIIHD ALSSTVRRAI TSGQDVNTAA GTAPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVM NRNGVLEATI SHFFSRSGL VGVVNLTDGG TDTTGYAVWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TENGEARPFM LQYMYVPPGA P KPTGRDAF ...String:
GDPVEDIIHD ALSSTVRRAI TSGQDVNTAA GTAPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVM NRNGVLEATI SHFFSRSGL VGVVNLTDGG TDTTGYAVWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TENGEARPFM LQYMYVPPGA P KPTGRDAF QWQTATNPSV FVKLTDPPAQ VSVPFMSPAS AYQWFYDGYP TFGQHPETSN TTYGQCPNNM MGTFAVRVVS RV ASQLKLQ TRVYMKLKHV RAWIPRPIRS QPYLLKNFPN YDSSKITYSA RDRASIKQAN M

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 27.72998 KDa
SequenceString: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVLAGRGSNT KPNEAPHPGF NTTFPGTAGA S FNDPYVLD ...String:
SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVLAGRGSNT KPNEAPHPGF NTTFPGTAGA S FNDPYVLD SGVPLSQSLI YPHQWINLRT NNCATIIVPY INAVPFDSAI NHSNFGLIVV PVSPLKYSSG ATTAIPITVT IA PLNSEFG GLRQAVSQ

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 26.219672 KDa
SequenceString: GLPTELRPGT NQFLTTEDDT AAPILPGFSP TPSIHIPGEV RSLLELCRVE TILEVNNTTD ATGLNRLLIP VSAQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP ...String:
GLPTELRPGT NQFLTTEDDT AAPILPGFSP TPSIHIPGEV RSLLELCRVE TILEVNNTTD ATGLNRLLIP VSAQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP WISNTHFRTA KTGGNYDYYT AGVVTLWYQT NYVVPPETPG EAYIIAMGAA QDNFTLKICK DTDEVTQQAV LQ

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5c4w

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1578

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