+Open data
-Basic information
Entry | Database: PDB / ID: 7e5r | ||||||
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Title | SARS-CoV-2 S trimer with three-antibody cocktail complex | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Complex / Antibody / VIRUS / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Sun, Y. / Wang, L. / Wang, N. / Feng, R. / Wang, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2021 Title: Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms. Authors: Yao Sun / Lei Wang / Rui Feng / Nan Wang / Yuxi Wang / Dandan Zhu / Xiaorui Xing / Peng Yang / Yanjun Zhang / Weimin Li / Xiangxi Wang / | ||||||
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 | 7e5r.cif.gz | 906.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e5r.ent.gz | 752.2 KB | Display | PDB format |
PDBx/mmJSON format | 7e5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e5r_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7e5r_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7e5r_validation.xml.gz | 116.3 KB | Display | |
Data in CIF | 7e5r_validation.cif.gz | 183 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/7e5r ftp://data.pdbj.org/pub/pdb/validation_reports/e5/7e5r | HTTPS FTP |
-Related structure data
Related structure data | 30993MC 7e5sC 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
-Protein , 2 types, 6 molecules LNOABC
#2: Protein | Mass: 23823.584 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #3: Protein | Mass: 141437.406 Da / Num. of mol.: 3 / Mutation: R682G, R683S, R685S, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) References: UniProt: P0DTC2 |
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-Antibody , 5 types, 15 molecules HDEMTIUVKRSQWXP
#1: Antibody | Mass: 23288.979 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #4: Antibody | Mass: 13165.724 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #5: Antibody | Mass: 11622.839 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #6: Antibody | Mass: 11217.353 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #7: Antibody | Mass: 13289.744 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) |
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-Sugars , 1 types, 15 molecules
#8: 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 |
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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
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Source (natural) |
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Source (recombinant) |
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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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92127 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.6 Å | ||||||||||||||||||||||||
Refine LS restraints |
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