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- PDB-6nb5: Crystal structure of anti- MERS-CoV human neutralizing LCA60 anti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nb5 | ||||||
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Title | Crystal structure of anti- MERS-CoV human neutralizing LCA60 antibody Fab fragment | ||||||
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![]() | IMMUNE SYSTEM / Fab / Coronavirus / MERS-CoV / Glycoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Walls, A.J. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, J. / Quispe, J. / Cameroni, E. / Gopal, R. / Dai, M. / Lanzavecchia, A. ...Walls, A.J. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, J. / Quispe, J. / Cameroni, E. / Gopal, R. / Dai, M. / Lanzavecchia, A. / Zambon, M. / Rey, F.A. / Corti, D. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / ...Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / Félix A Rey / Davide Corti / David Veesler / ![]() ![]() ![]() ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.5 KB | Display | ![]() |
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PDB format | ![]() | 134 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0401C ![]() 0402C ![]() 0403C ![]() 0404C ![]() 6nb3C ![]() 6nb4C ![]() 6nb6C ![]() 6nb7C ![]() 6nb8C ![]() 6c5vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24516.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 22545.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 30 % (v/v) Jeffamine ED-2001 pH 7.0 and 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2018 | ||||||||||||||||||||||||
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3→39.18 Å / Num. obs: 17505 / % possible obs: 99.6 % / Redundancy: 3.1 % / CC1/2: 0.927 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.197 / Rrim(I) all: 0.354 / Net I/σ(I): 3.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6C5V Resolution: 3→39.18 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.828 / SU B: 36.119 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.337 Å2
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Refinement step | Cycle: 1 / Resolution: 3→39.18 Å
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Refine LS restraints |
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