+Open data
-Basic information
Entry | Database: PDB / ID: 6aku | ||||||
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Title | Cryo-EM structure of CVA10 empty particle | ||||||
Components |
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Keywords | VIRUS / picornavirus uncoating / receptor binding | ||||||
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 / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus 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 / virus-mediated perturbation of host defense response / 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 | ||||||
Biological species | Coxsackievirus A10 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Zhu, L. / Sun, Y. / Fan, J.Y. / Zhu, B. / Cao, L. / Gao, Q. / Zhang, Y.J. / Liu, H.R. / Rao, Z.H. / Wang, X.X. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating. Authors: Ling Zhu / Yao Sun / Jinyan Fan / Bin Zhu / Lei Cao / Qiang Gao / Yanjun Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang / Abstract: Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, ...Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, utilizing the molecule KREMEN1 as an entry receptor, constitutes a KREMEN1-dependent subgroup within HEV-As. Currently, there is no vaccine or antiviral therapy available for treating diseases caused by CVA10. The atomic-resolution structure of the CVA10 virion, which is within the KREMEN1-dependent subgroup, shows significant conformational differences in the putative receptor binding sites and serotype-specific epitopes, when compared to the SCARB2-dependent subgroup of HEV-A, such as EV71, highlighting specific differences between the sub-groups. We also report two expanded structures of CVA10, an empty particle and uncoating intermediate at atomic resolution, as well as a medium-resolution genome structure reconstructed using a symmetry-mismatch method. Structural comparisons coupled with previous results, reveal an ordered signal transmission process for enterovirus uncoating, converting exo-genetic receptor-attachment inputs into a generic RNA release mechanism. | ||||||
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 | 6aku.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aku.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 6aku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aku_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6aku_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6aku_validation.xml.gz | 25 KB | Display | |
Data in CIF | 6aku_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6aku ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6aku | HTTPS FTP |
-Related structure data
Related structure data | 9644MC 9642C 9643C 9652C 6aksC 6aktC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 33232.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: W0G0K3 |
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#2: Protein | Mass: 27783.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A0C5AZ80 |
#3: Protein | Mass: 26279.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A10 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A0C5AWF6 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Coxsackievirus A10 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Coxsackievirus A10 |
Source (recombinant) | Organism: Chlorocebus aethiops (grivet) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22725 / Symmetry type: POINT | ||||||||||||||||||||||||
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