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Open data
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Basic information
Entry | Database: PDB / ID: 7ybl | ||||||
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Title | SARS-CoV-2 B.1.620 variant spike (close state) | ||||||
![]() | Spike glycoprotein | ||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / Lambda / spike | ||||||
Function / homology | ![]() 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 / symbiont-mediated suppression of host innate immune response / structural constituent of virion ...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 / symbiont-mediated suppression of host innate immune response / 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 / 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Wang, X. / Fu, W. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants. Authors: Xiaorui Xing / Lei Wang / Zhen Cui / Wangjun Fu / Tao Zheng / Lili Qin / Pingju Ge / Aidong Qian / Nan Wang / Shuai Yuan / ![]() Abstract: • Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift. • T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more ...• Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift. • T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult. • The overall structures of the closed state S complex from different variants resemble each other. • Mutations in FPPR may affect the overall structure of the trimeric spike protein. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 603.9 KB | Display | ![]() |
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PDB format | ![]() | 495.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 91.5 KB | Display | |
Data in CIF | ![]() | 138.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33725MC ![]() 7ybhC ![]() 7ybiC ![]() 7ybjC ![]() 7ybkC ![]() 7ybmC ![]() 7ybnC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 140983.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #2: 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 #3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 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 |
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Sample preparation
Component | Name: SARS-CoV-2 B.1.620 variant spike (close state) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315257 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.6 Å | ||||||||||||||||||||||||
Refine LS restraints |
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