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- PDB-7e9n: Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e9n | |||||||||
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Title | Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 down RBD, state1) | |||||||||
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![]() | VIRAL PROTEIN / IMMUNE SYSTEM | |||||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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: 3.69 Å | |||||||||
![]() | Wang, X.F. / Zhu, Y.Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD Authors: Wang, X. / Hu, A. / Chen, X. / Zhang, Y. / Yu, F. / Yue, S. / Li, A. / Zhang, J. / Pan, Z. / Yang, Y. / Lin, Y. / Gao, L. / Zhou, J. / Zhao, J. / Li, F. / Shi, Y. / Huang, F. / Yang, X. / ...Authors: Wang, X. / Hu, A. / Chen, X. / Zhang, Y. / Yu, F. / Yue, S. / Li, A. / Zhang, J. / Pan, Z. / Yang, Y. / Lin, Y. / Gao, L. / Zhou, J. / Zhao, J. / Li, F. / Shi, Y. / Huang, F. / Yang, X. / Peng, Y. / Tu, L. / Zhang, H. / Zheng, H. / He, J. / Zhang, H. / Xu, L. / Huang, Q. / Zhu, Y. / Deng, K. / Ye, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 743.6 KB | Display | ![]() |
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PDB format | ![]() | 609.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 845 KB | Display | ![]() |
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Full document | ![]() | 927.1 KB | Display | |
Data in XML | ![]() | 112.6 KB | Display | |
Data in CIF | ![]() | 177.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31033MC ![]() 7e9pC ![]() 7enfC ![]() 7engC ![]() 7f46C 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: 124152.539 Da / Num. of mol.: 3 / Mutation: F817P, A892P, A899P, A942P, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Cell line (production host): HEK293 / Production host: ![]() #2: Antibody | Mass: 23802.490 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 25139.314 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: 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: Complex of the SARS-CoV-2 S-6P with 35B5 Fab(1 down RBD, state1) Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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: BRIGHT FIELD / Nominal defocus max: 1300 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62600 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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