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- PDB-8zhl: SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8zhl | ||||||||||||
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Title | SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs | ||||||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
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 / 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 | ![]() ![]() ![]() synthetic construct (others) ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||||||||
![]() | Yan, Q. / Gao, X. / Liu, B. / Hou, R. / He, P. / Li, Z. / Chen, Q. / Wang, J. / He, J. / Chen, L. ...Yan, Q. / Gao, X. / Liu, B. / Hou, R. / He, P. / Li, Z. / Chen, Q. / Wang, J. / He, J. / Chen, L. / Zhao, J. / Xiong, X. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants Authors: Yan, Q. / Gao, X. / Liu, B. / Hou, R. / He, P. / Ma, Y. / Zhang, Y. / Zhang, Y. / Li, Z. / Chen, Q. / Wang, J. / Huang, X. / Liang, H. / Zheng, H. / Yao, Y. / Chen, X. / Niu, X. / He, J. / ...Authors: Yan, Q. / Gao, X. / Liu, B. / Hou, R. / He, P. / Ma, Y. / Zhang, Y. / Zhang, Y. / Li, Z. / Chen, Q. / Wang, J. / Huang, X. / Liang, H. / Zheng, H. / Yao, Y. / Chen, X. / Niu, X. / He, J. / Chen, L. / Zhao, J. / Xiong, X. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 60107MC ![]() 8zhdC ![]() 8zheC ![]() 8zhfC ![]() 8zhgC ![]() 8zhhC ![]() 8zhiC ![]() 8zhjC ![]() 8zhkC ![]() 8zhmC ![]() 8zhnC ![]() 8zhoC ![]() 8zhpC C: citing same article ( M: map data used to model this data |
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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 141253.875 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2, wac, EcT6_00157 / Cell line (production host): Expi293F / Production host: ![]() |
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-Antibody , 4 types, 8 molecules HGLIDKEM
#2: Antibody | Mass: 23840.717 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 22382.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 25768.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Antibody | Mass: 25868.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 45 molecules ![](data/chem/img/NAG.gif)
#6: 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 #7: Sugar | ChemComp-NAG / |
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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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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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: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19648 / Symmetry type: POINT |