+Open data
-Basic information
Entry | Database: PDB / ID: 6u7h | |||||||||
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Title | Cryo-EM structure of the HCoV-229E spike glycoprotein | |||||||||
Components | spike glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / CoV coronavirus 229E / spike glycoprotein / APN | |||||||||
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 / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Human coronavirus 229E | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li, Z. / Benlekbir, S. / Rubinstein, J.L. / Rini, J.M. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Elife / Year: 2019 Title: The human coronavirus HCoV-229E S-protein structure and receptor binding. Authors: Zhijie Li / Aidan Ca Tomlinson / Alan Hm Wong / Dongxia Zhou / Marc Desforges / Pierre J Talbot / Samir Benlekbir / John L Rubinstein / James M Rini / Abstract: The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S- ...The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion. | |||||||||
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 | 6u7h.cif.gz | 518.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u7h.ent.gz | 430.2 KB | Display | PDB format |
PDBx/mmJSON format | 6u7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u7h_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6u7h_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6u7h_validation.xml.gz | 77.8 KB | Display | |
Data in CIF | 6u7h_validation.cif.gz | 121.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/6u7h ftp://data.pdbj.org/pub/pdb/validation_reports/u7/6u7h | HTTPS FTP |
-Related structure data
Related structure data | 20668MC 6u7eC 6u7fC 6u7gC 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
#1: Protein | Mass: 127231.117 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus 229E / Strain: VR-740 / Plasmid: PB-T-PAF / Cell line (production host): HEK-293 Freestyle / Production host: Homo sapiens (human) / References: UniProt: P15423*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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: Human coronavirus 229E spike glycoprotein / Type: COMPLEX Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.38 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Human coronavirus 229E | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||
Specimen support | Details: 15 micro Ampere / Grid material: COPPER / Grid mesh size: 400 divisions/in. | |||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 295 K / Details: Blot for 13 seconds before plunging |
-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 / Nominal magnification: 75000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 42.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
-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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71350 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Manual model building was done in COOT and ChimeraX/ISOLDE. A homology model based on PDB:5SZS was used as a reference during model building. | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5SZS Pdb chain-ID: A | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.43 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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