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- PDB-6nb6: SARS-CoV complex with human neutralizing S230 antibody Fab fragme... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nb6 |
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Title | SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1) |
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Function / homology | Coronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...Coronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host endosome membrane / ![]() ![]() ![]() ![]() ![]() |
Specimen source | ![]() ![]() ![]() ![]() |
Method | ![]() ![]() ![]() |
![]() | Walls, A.C. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, S. / Quispe, J. / Cameroni, E. / Gopal, R. / Mian, D. / Lanzavecchia, A. / Zambon, M. / Rey, F.A. / Corti, D. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) |
![]() | Journal: Cell / Year: 2019 Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. ![]() Abstract: Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways ...Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism. |
Validation Report | ![]() ![]() ![]() |
Date | Deposition: Dec 6, 2018 / Release: Feb 6, 2019 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
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Links
-Related structure data
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein/peptide , 3 types, 7 molecules ABCHILM
#1: Protein/peptide | Mass: 139815.969 Da / Num. of mol.: 3 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 14314.899 Da / Num. of mol.: 2 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 12329.663 Da / Num. of mol.: 2 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 149 molecules 




#4: Chemical | ChemComp-NAG / #5: Chemical | ChemComp-BMA / #6: Chemical | ChemComp-MAN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: ![]() |
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Sample preparation
Component | Name: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1) Type: COMPLEX / Entity ID: 1, Molecular weight | Value: 572 MDa / Experimental value: YES | Source (natural) | Organism: | ![]() ![]() Source (recombinant) | Organism: | ![]() ![]() Buffer solution | pH: 8 | Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied | ![]() ![]() 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 | Microscope model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23071 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Ref protocol: OTHER / Ref space: REAL |