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Yorodumi- PDB-8bev: Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bev | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD) | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / spike / S protein / HexaPro / nanobody | ||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Vicugna pacos (alpaca) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.92 Å | ||||||
Authors | Lauer, S. / Spahn, C.M.T. / Schwefel, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD) Authors: Schwefel, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bev.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bev.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8bev ftp://data.pdbj.org/pub/pdb/validation_reports/be/8bev | HTTPS FTP |
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-Related structure data
Related structure data | 16010MC 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
#1: Protein | Mass: 140539.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): Flp-In TRex 293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | | Mass: 17827.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: LOC102538064 / Production host: Escherichia coli (E. coli) #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #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: Severe acute respiratory syndrome coronavirus 2 spike protein in complex with nanobody W25 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.14 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Strain: Flp-In TRex 293 | |||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 277 K / Details: 1s blotting time |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal magnification: 31000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2080 |
Image scans | Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 527691 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132634 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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