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- EMDB-10263: Structure of Coxsackievirus A10 complexed with its receptor KREMEN1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10263
TitleStructure of Coxsackievirus A10 complexed with its receptor KREMEN1
Map data
SampleCoxsackievirus A10:
KREMEN1 / (Capsid protein ...Capsid) x 2 / (Coxsackievirus ...) x 2 / Kremen protein 1 / (ligand) x 2
Function / homology
Function and homology information


Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / limb development / regulation of canonical Wnt signaling pathway / suppression by virus of host MDA-5 activity / picornain 2A / pore-mediated entry of viral genome into host cell ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / limb development / regulation of canonical Wnt signaling pathway / suppression by virus of host MDA-5 activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / TCF dependent signaling in response to WNT / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell / negative regulation of canonical Wnt signaling pathway / protein complex oligomerization / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / Wnt signaling pathway / suppression by virus of host gene expression / ion channel activity / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / neuronal cell body / apoptotic process / structural molecule activity / RNA binding / membrane / integral component of membrane / ATP binding / plasma membrane / metal ion binding
Similarity search - Function
Kremen / Carbohydrate-binding WSC / WSC domain / present in yeast cell wall integrity and stress response component proteins / WSC domain profile. / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Kremen / Carbohydrate-binding WSC / WSC domain / present in yeast cell wall integrity and stress response component proteins / WSC domain profile. / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Poliovirus 3A protein like / Poliovirus 3A protein-like / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 / Kringle domain / Kringle / Kringle domain signature. / Kringle superfamily / Kringle domain / Kringle, conserved site / Kringle domain profile. / 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 / Kringle-like fold / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Kremen protein 1
Similarity search - Component
Biological speciesCoxsackievirus A10 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 27, 2019-
Header (metadata) releaseSep 4, 2019-
Map releaseJan 15, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6snw
  • Surface level: 0.01
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6snw
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10263.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å
1.35 Å/pix.
x 400 pix.
= 540. Å
1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.05129708 - 0.097188205
Average (Standard dev.)0.0006619525 (±0.0049746973)
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-0.0510.0970.001

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Supplemental data

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Sample components

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Entire Coxsackievirus A10

EntireName: Coxsackievirus A10 / Number of components: 10

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Component #1: protein, Coxsackievirus A10

ProteinName: Coxsackievirus A10 / Recombinant expression: No

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Component #2: protein, Coxsackievirus A10

ProteinName: Coxsackievirus A10 / Recombinant expression: No
SourceSpecies: Coxsackievirus A10 / Strain: Kowalik

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Component #3: protein, KREMEN1

ProteinName: KREMEN1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293S

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Component #4: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.191422 kDa
SourceSpecies: Coxsackievirus A10

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Component #5: protein, Coxsackievirus VP2

ProteinName: Coxsackievirus VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.72998 kDa
SourceSpecies: Coxsackievirus A10

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Component #6: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.219672 kDa
SourceSpecies: Coxsackievirus A10

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Component #7: protein, Coxsackievirus VP4

ProteinName: Coxsackievirus VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.464065 kDa
SourceSpecies: Coxsackievirus A10

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Component #8: protein, Kremen protein 1

ProteinName: Kremen protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.786293 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Component #10: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1597
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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