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Yorodumi- PDB-6nzk: Structural basis for human coronavirus attachment to sialic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nzk | |||||||||
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Title | Structural basis for human coronavirus attachment to sialic acid receptors | |||||||||
Components | Spike surface glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / Coronavirus spike glycoprotein / sialic acid / HCoV-OC43 / fusion protein | |||||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Human coronavirus OC43 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Tortorici, M.A. / Walls, A.C. / Lang, Y. / Wang, C. / Li, Z. / Koerhuis, D. / Boons, G.J. / Bosch, B.J. / Rey, F.A. / de Groot, R. / Veesler, D. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structural basis for human coronavirus attachment to sialic acid receptors. Authors: M Alejandra Tortorici / Alexandra C Walls / Yifei Lang / Chunyan Wang / Zeshi Li / Danielle Koerhuis / Geert-Jan Boons / Berend-Jan Bosch / Félix A Rey / Raoul J de Groot / David Veesler / Abstract: Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host ...Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host receptors and fuses the viral and cellular membranes. To understand the molecular basis of coronavirus attachment to oligosaccharide receptors, we determined cryo-EM structures of coronavirus OC43 S glycoprotein trimer in isolation and in complex with a 9-O-acetylated sialic acid. We show that the ligand binds with fast kinetics to a surface-exposed groove and that interactions at the identified site are essential for S-mediated viral entry into host cells, but free monosaccharide does not trigger fusogenic conformational changes. The receptor-interacting site is conserved in all coronavirus S glycoproteins that engage 9-O-acetyl-sialogycans, with an architecture similar to those of the ligand-binding pockets of coronavirus hemagglutinin esterases and influenza virus C/D hemagglutinin-esterase fusion glycoproteins. Our results demonstrate these viruses evolved similar strategies to engage sialoglycans at the surface of target cells. | |||||||||
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 | 6nzk.cif.gz | 723.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nzk.ent.gz | 588.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nzk_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6nzk_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6nzk_validation.xml.gz | 94.6 KB | Display | |
Data in CIF | 6nzk_validation.cif.gz | 149 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/6nzk ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nzk | HTTPS FTP |
-Related structure data
Related structure data | 0557MC 6ohwC 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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1 |
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-Components
-Protein / Non-polymers , 2 types, 399 molecules ABC
#1: Protein | Mass: 146438.312 Da / Num. of mol.: 3 / Mutation: R754G,R755G,R757G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus OC43 / Production host: Homo sapiens (human) / References: UniProt: Q696P8 #7: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 48 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: Sugar | ChemComp-NAG / #6: Sugar | |
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-Details
Has protein modification | 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: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Betacoronavirus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: C-flat-1.2/1.3 4C |
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: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178356 / Symmetry type: POINT |