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Yorodumi- PDB-6snw: Structure of Coxsackievirus A10 complexed with its receptor KREMEN1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6snw | ||||||||||||
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Title | Structure of Coxsackievirus A10 complexed with its receptor KREMEN1 | ||||||||||||
Components |
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Keywords | VIRUS / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / neuronal cell body / virion attachment to host cell / apoptotic process / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Coxsackievirus A10 | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Zhao, 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
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6snw.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6snw.ent.gz | 163.1 KB | Display | PDB format |
PDBx/mmJSON format | 6snw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6snw_validation.pdf.gz | 896.7 KB | Display | wwPDB validaton report |
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Full document | 6snw_full_validation.pdf.gz | 900.2 KB | Display | |
Data in XML | 6snw_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 6snw_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/6snw ftp://data.pdbj.org/pub/pdb/validation_reports/sn/6snw | HTTPS FTP |
-Related structure data
Related structure data | 10263MC 6smgC 6snbC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Capsid protein ... , 2 types, 2 molecules AC
#1: Protein | 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 |
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#3: Protein | 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 |
-Coxsackievirus ... , 2 types, 2 molecules BD
#2: Protein | 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 |
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#4: Protein | 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 |
-Protein / Non-polymers / Sugars , 3 types, 4 molecules E
#5: Protein | 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 |
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#6: Chemical | ChemComp-SPH / |
#7: Sugar |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S | ||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: PHENIX / Version: dev_3488: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1597 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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