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Yorodumi- PDB-6la5: Cryo-EM structure of echovirus 11 complexed with its attaching re... -
+Open data
-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 | ||||||
Components |
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Keywords | VIRUS / Cryo-EM structure / echovirus 11 / CD55 / pH 7.4 | ||||||
Function / homology | Function and homology information negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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 ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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 / COPI-mediated anterograde transport / side of membrane / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / secretory granule membrane / T=pseudo3 icosahedral viral capsid / 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 / virus receptor activity / protein complex oligomerization / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / RNA helicase activity / DNA replication / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / Golgi membrane / RNA-dependent RNA polymerase activity / innate immune 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Echovirus E11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
Authors | Liu, S. / Gao, F.G. | ||||||
Citation | Journal: Chin.Sci.Bull. / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6la5.cif.gz | 176.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6la5.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 6la5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6la5 ftp://data.pdbj.org/pub/pdb/validation_reports/la/6la5 | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-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) Echovirus E11 / References: UniProt: Q2LJ73*PLUS |
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#2: Protein | Mass: 27968.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A0R5YS56*PLUS |
#3: Protein | Mass: 26062.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A346I7K2*PLUS |
#4: Protein | Mass: 7495.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: E0WN77*PLUS |
-Protein / Non-polymers , 2 types, 2 molecules E
#5: Protein | Mass: 13586.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Production host: Homo sapiens (human) / References: UniProt: P08174 |
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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 |
-Sample preparation
Component | Name: Echovirus E11 / Type: VIRUS / Entity ID: #2-#5 / Source: NATURAL |
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Source (natural) | Organism: Echovirus E11 |
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 |
-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 FIELDBright-field microscopy |
Image recording | Electron dose: 1.025 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-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 | ||||||||||||||||||||||||
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