+Open data
-Basic information
Entry | Database: PDB / ID: 7xy4 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike in complex with VHH21 | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / spike / SARS-CoV-2 / coronavirus / glycoprotein / nanobody / VHH21 / complex / VIRAL PROTEIN / Cryo-EM / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 Camelus bactrianus (Bactrian camel) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Cao, D. / Fan, X. / Zhang, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Identification of nano-abzymes to catalyze the spike-trimer of SARS-CoV-2 Authors: Wang, K. / Cao, D. / Liu, L. / Fan, X. / Wang, H. / Zhang, X. / Yang, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xy4.cif.gz | 611.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xy4.ent.gz | 496.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xy4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7xy4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xy4_validation.xml.gz | 93.9 KB | Display | |
Data in CIF | 7xy4_validation.cif.gz | 143.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xy4 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xy4 | HTTPS FTP |
-Related structure data
Related structure data | 33510MC 7xy3C 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: 125410.047 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 #2: Antibody | Mass: 16421.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli) #3: 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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 302560 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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