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Yorodumi- PDB-7ej4: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutraliz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ej4 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25 | ||||||||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / Spike protein / Neutralizing antibody | ||||||||||||||||||||||||||||||
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 / membrane fusion / Attachment and Entry / 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 Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||||||||||||||
Authors | Yang, T.J. / Yu, P.Y. / Wu, H.C. / Hsu, S.T.D. | ||||||||||||||||||||||||||||||
Funding support | Taiwan, 9items
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Citation | Journal: To be published Title: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25 Authors: Yang, T.J. / Yu, P.Y. / Wu, H.C. / Hsu, S.T.D. | ||||||||||||||||||||||||||||||
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 | 7ej4.cif.gz | 707.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ej4.ent.gz | 569.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ej4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ej4_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7ej4_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7ej4_validation.xml.gz | 97.5 KB | Display | |
Data in CIF | 7ej4_validation.cif.gz | 151.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7ej4 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ej4 | HTTPS FTP |
-Related structure data
Related structure data | 30669MC 7ej5C 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: 142236.328 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 48952.828 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23415.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #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: SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25 Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: YES | ||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s |
-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 / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102537 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 184.3 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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