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- PDB-6snw: Structure of Coxsackievirus A10 complexed with its receptor KREMEN1 -

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Basic information

Entry
Database: PDB / ID: 6snw
TitleStructure of Coxsackievirus A10 complexed with its receptor KREMEN1
Components
  • (Capsid protein ...Capsid) x 2
  • (Coxsackievirus ...) x 2
  • Kremen protein 1
KeywordsVIRUS / CV-A10 / KREMEN1 / Virus-receptor complex / Hand / foot and mouth disease / picornavirus uncoating intermediate
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 / regulation of canonical Wnt signaling pathway / limb development / 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 ...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 / regulation of canonical Wnt signaling pathway / limb development / 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 / TCF dependent signaling in response to WNT / host cell cytoplasmic vesicle membrane / negative regulation of canonical Wnt signaling pathway / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / Wnt signaling pathway / : / 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 / neuronal cell body / DNA-templated transcription / apoptotic process / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Kremen / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain ...Kremen / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Jelly Rolls - #20 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 / Jelly Rolls / 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 / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
SPHINGOSINE / Genome polyprotein / Kremen protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus A10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhao, Y. / Zhou, D. / Ni, T. / Karia, D. / Kotecha, A. / Wang, X. / Rao, Z. / Jones, E.Y. / Fry, E.E. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
Cancer Research UKC375/A17721 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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Assembly

Deposited unit
A: Capsid protein VP1
B: Coxsackievirus VP2
C: Capsid protein VP3
D: Coxsackievirus VP4
E: Kremen protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1338
Polymers136,3915
Non-polymers7423
Water0
1
A: Capsid protein VP1
B: Coxsackievirus VP2
C: Capsid protein VP3
D: Coxsackievirus VP4
E: Kremen protein 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,228,000480
Polymers8,183,486300
Non-polymers44,514180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

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Capsid protein ... , 2 types, 2 molecules AC

#1: Protein Capsid protein VP1 /


Mass: 33191.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10
References: UniProt: Q6JKR9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Capsid protein VP3 /


Mass: 26219.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10
References: UniProt: Q6JKR9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Coxsackievirus ... , 2 types, 2 molecules BD

#2: Protein Coxsackievirus VP2


Mass: 27729.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10
References: UniProt: Q6JKR9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Coxsackievirus VP4


Mass: 7464.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10
References: UniProt: Q6JKR9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Protein / Non-polymers / Sugars , 3 types, 4 molecules E

#5: Protein Kremen protein 1 / Dickkopf receptor / Kringle domain-containing transmembrane protein 1 / Kringle-containing protein ...Dickkopf receptor / Kringle domain-containing transmembrane protein 1 / Kringle-containing protein marking the eye and the nose


Mass: 41786.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KREMEN1, KREMEN, KRM1 / Cell (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96MU8
#6: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Coxsackievirus A10COMPLEX#1-#50MULTIPLE SOURCES
2Coxsackievirus A10COMPLEX#1-#41NATURAL
3KREMEN1COMPLEX#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Coxsackievirus A1042769Kowalik
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 8
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

SoftwareName: PHENIX / Version: dev_3488: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1597 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0098989
ELECTRON MICROSCOPYf_angle_d0.88412266
ELECTRON MICROSCOPYf_dihedral_angle_d13.5695301
ELECTRON MICROSCOPYf_chiral_restr0.0531336
ELECTRON MICROSCOPYf_plane_restr0.0051606

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