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Yorodumi- PDB-8fr7: A hinge glycan regulates spike bending and impacts coronavirus in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fr7 | |||||||||||||||||||||||||||
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Title | A hinge glycan regulates spike bending and impacts coronavirus infectivity | |||||||||||||||||||||||||||
Components | Spike glycoprotein | |||||||||||||||||||||||||||
Keywords | VIRAL PROTEIN / NL63 / coronavirus / glycan | |||||||||||||||||||||||||||
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 / host cell surface receptor binding / 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 NL63 | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | |||||||||||||||||||||||||||
Authors | Pintilie, G. / Wilson, E. / Chmielewski, D. / Schmid, M.F. / Jin, J. / Chen, M. / Singharoy, A. / Chiu, W. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: To Be Published Title: A hinge glycan regulates spike bending and impacts coronavirus infectivity Authors: Chmielewski, D. / Wilson, E. / Pintilie, G. / Chen, M. / Schmid, M.F. / Wells, L. / Jin, J. / Singharoy, A. / Chiu, W. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fr7.cif.gz | 895.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fr7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fr7_validation.pdf.gz | 7.1 MB | Display | wwPDB validaton report |
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Full document | 8fr7_full_validation.pdf.gz | 7.3 MB | Display | |
Data in XML | 8fr7_validation.xml.gz | 128 KB | Display | |
Data in CIF | 8fr7_validation.cif.gz | 193.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/8fr7 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/8fr7 | HTTPS FTP |
-Related structure data
Related structure data | 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 , 1 types, 3 molecules ACB
#1: Protein | Mass: 149954.109 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Gene: S, 2 / Cell line (production host): Vero E6 / Organ (production host): kidney / Production host: Chlorocebus pygerythrus (vervet) / References: UniProt: Q6Q1S2 |
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-Sugars , 9 types, 119 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 Source method: isolated from a genetically manipulated source #4: Polysaccharide | Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Type: oligosaccharide / Mass: 2152.965 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source |
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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: HCoV-NL63 spike trimer / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.6 MDa / Experimental value: YES |
Source (natural) | Organism: unidentified human coronavirus |
Buffer solution | pH: 8 / Details: 20 mM Tris, pH 8.0, 120 mM NaCl, 1 mM EDTA |
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: HCoV-NL63 virions |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
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 / Nominal magnification: 64000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 30000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4138 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 944822 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82030 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |