+Open data
-Basic information
Entry | Database: PDB / ID: 7fcd | ||||||
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Title | Structure of the SARS-CoV-2 A372T spike glycoprotein (open) | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 spike | ||||||
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 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Wang, X. / Zhang, S. | ||||||
Funding support | 1items
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Citation | Journal: Cell Res / Year: 2022 Title: Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2. Authors: Shuyuan Zhang / Qingtai Liang / Xinheng He / Chongchong Zhao / Wenlin Ren / Ziqing Yang / Ziyi Wang / Qiang Ding / Haiteng Deng / Tong Wang / Linqi Zhang / Xinquan 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 | 7fcd.cif.gz | 555 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fcd.ent.gz | 448.7 KB | Display | PDB format |
PDBx/mmJSON format | 7fcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fcd_validation.pdf.gz | 838.3 KB | Display | wwPDB validaton report |
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Full document | 7fcd_full_validation.pdf.gz | 889 KB | Display | |
Data in XML | 7fcd_validation.xml.gz | 85.1 KB | Display | |
Data in CIF | 7fcd_validation.cif.gz | 127.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/7fcd ftp://data.pdbj.org/pub/pdb/validation_reports/fc/7fcd | HTTPS FTP |
-Related structure data
Related structure data | 31524MC 7fceC 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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-Components
#1: Protein | Mass: 143570.500 Da / Num. of mol.: 3 / Mutation: A372T, 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: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Sugar | ChemComp-NAG / Has ligand of interest | N | Has protein modification | Y | |
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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 A372T spike / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 1.5 mg/ml / 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55181 / Symmetry type: POINT |