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- PDB-6la5: Cryo-EM structure of echovirus 11 complexed with its attaching re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6la5 | ||||||
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Title | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | ||||||
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![]() | VIRUS / Cryo-EM structure / echovirus 11 / CD55 / pH 7.4 | ||||||
Function / homology | ![]() regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / secretory granule membrane / T=pseudo3 icosahedral viral capsid / complement activation, classical pathway / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / symbiont-mediated suppression of host gene expression / positive regulation of cytosolic calcium ion concentration / DNA replication / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / viral RNA genome replication / Golgi membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
![]() | Liu, S. / Gao, F.G. | ||||||
![]() | ![]() Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Authors: Niu, S. / Liu, C. / Liu, C. / Liu, S. / Song, Y. / Zhang, Y. / Tian, W. / Zhao, X. / Wang, P. / Gao, F.G. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.3 KB | Display | ![]() |
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PDB format | ![]() | 144 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1009 KB | Display | ![]() |
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Full document | ![]() | 1019.1 KB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0856MC ![]() 0854C ![]() 0855C ![]() 0857C ![]() 0858C ![]() 0859C ![]() 0860C ![]() 0867C ![]() 0870C ![]() 0871C ![]() 6la3C ![]() 6la4C ![]() 6la6C ![]() 6la7C ![]() 6laoC ![]() 6lapC ![]() 6lb1C ![]() 6lboC ![]() 6lbqC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
-Capsid protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32277.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 27968.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 26062.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 7495.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein / Non-polymers , 2 types, 2 molecules E![](data/chem/img/SPH.gif)
![](data/chem/img/SPH.gif)
#5: Protein | Mass: 13586.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#6: Chemical | ChemComp-SPH / |
-Details
Has ligand of interest | Y |
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Sequence details | THE VIRUS WAS ISOLATED FROM CHINA, AND THE GENEBANK: MN496161. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Echovirus E11 / Type: VIRUS / Entity ID: #2-#5 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.025 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25524 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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