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Yorodumi- PDB-8b8r: Complex of Echovirus 11 with its attaching receptor decay-acceler... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b8r | ||||||
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Title | Complex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55) | ||||||
Components |
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Keywords | VIRUS / Echovirus / receptor / DAF / CD55 | ||||||
Function / homology | SPHINGOSINE Function and homology information | ||||||
Biological species | Homo sapiens (human) Echovirus E11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Stuart, D.I. / Ren, J. / Zhou, D. / Qin, L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Viruses / Year: 2022 Title: Switching of Receptor Binding Poses between Closely Related Enteroviruses. Authors: Daming Zhou / Ling Qin / Helen M E Duyvesteyn / Yuguang Zhao / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Kuan-Ying A Huang / David I Stuart / Abstract: Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity ...Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating factor (DAF, also known as CD55) is an attachment receptor for E11. Here, we report the structure of the complex of E11 and the full-length ectodomain of DAF (short consensus repeats, SCRs, 1-4) at 3.1 Å determined by cryo-electron microscopy (cryo-EM). SCRs 3 and 4 of DAF interact with E11 at the southern rim of the canyon via the VP2 EF and VP3 BC loops. We also observe an unexpected interaction between the N-linked glycan (residue 95 of DAF) and the VP2 BC loop of E11. DAF is a receptor for at least 20 enteroviruses and we classify its binding patterns from reported DAF/virus complexes into two distinct positions and orientations, named as E6 and E11 poses. Whilst 60 DAF molecules can attach to the virion in the E6 pose, no more than 30 can attach to E11 due to steric restrictions. Analysis of the distinct modes of interaction and structure and sequence-based phylogenies suggests that the two modes evolved independently, with the E6 mode likely found earlier. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b8r.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b8r.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/8b8r ftp://data.pdbj.org/pub/pdb/validation_reports/b8/8b8r | HTTPS FTP |
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-Related structure data
Related structure data | 15920MC 8b9fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 32838.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 |
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#2: Protein | Mass: 28886.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 |
#3: Protein | Mass: 26029.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 |
#4: Protein | Mass: 7498.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 |
#5: Protein | Mass: 29771.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-SPH / |
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-Details
Has ligand of interest | Y |
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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
Component | Name: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55) Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Echovirus E11 |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: SPOT SCAN |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 3000 nm |
Image recording | Electron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6394 / Symmetry type: POINT |