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Yorodumi- PDB-8tc1: Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 00... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tc1 | ||||||
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Title | Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 007 in Closed Conformation | ||||||
Components | Spike glycoproteinSpike protein | ||||||
Keywords | VIRAL PROTEIN / Spike / Glycoprotein / Coronavirus | ||||||
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 | Paguma larvata (masked palm civet) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.92 Å | ||||||
Authors | Bostina, M. / Hills, F.R. / Eruera, A.R. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: Cryo-EM reveals variationo in structural motifs within animal SARS-related coronavirus spike protein Authors: Bostina, M. / Hills, F.R. / Eruera, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tc1.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tc1.ent.gz | 987.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/8tc1 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/8tc1 | HTTPS FTP |
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-Related structure data
Related structure data | 41150MC 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 ABC
#1: Protein | Mass: 122479.953 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paguma larvata (masked palm civet) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q3ZTF3 |
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-Sugars , 3 types, 45 molecules
#2: 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 #3: 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 Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 585 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: Civet SARS CoV 007/2004 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Civet SARS CoV 007/2004 (virus) |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 8 |
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: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 800000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.08 Å2 | ||||||||||||||||||||||||
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