+Open data
-Basic information
Entry | Database: PDB / ID: 7kkj | ||||||
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Title | Structure of anti-SARS-CoV-2 Spike nanobody mNb6 | ||||||
Components | Synthetic nanobody mNb6 | ||||||
Keywords | IMMUNE SYSTEM / Complex / Nanobody / VHH | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Schoof, M.S. / Faust, B.F. / Saunders, R.A. / Sangwan, S. / Rezelj, V. / Hoppe, N. / Boone, M. / Billesboelle, C.B. / Puchades, C. / Azumaya, C.M. ...Schoof, M.S. / Faust, B.F. / Saunders, R.A. / Sangwan, S. / Rezelj, V. / Hoppe, N. / Boone, M. / Billesboelle, C.B. / Puchades, C. / Azumaya, C.M. / Kratochvil, H.T. / Zimanyi, M. / Desphande, I. / Liang, J. / Dickinson, S. / Nguyen, H.C. / Chio, C.M. / Merz, G.E. / Thompson, M.C. / Diwanji, D. / Schaefer, K. / Anand, A.A. / Dobzinski, N. / Zha, B.S. / Simoneau, C.R. / Leon, K. / White, K.M. / Chio, U.S. / Gupta, M. / Jin, M. / Li, F. / Liu, Y. / Zhang, K. / Bulkley, D. / Sun, M. / Smith, A.M. / Rizo, A.N. / Moss, F. / Brilot, A.F. / Pourmal, S. / Trenker, R. / Pospiech, T. / Gupta, S. / Barsi-Rhyne, B. / Belyy, V. / Barile-Hill, A.W. / Nock, S. / Liu, Y. / Krogan, N.J. / Ralston, C.Y. / Swaney, D.L. / Garcia-Sastre, A. / Ott, M. / Vignuzzi, M. / Walter, P. / Manglik, A. / QCRG Structural Biology Consortium | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2020 Title: An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Authors: Michael Schoof / Bryan Faust / Reuben A Saunders / Smriti Sangwan / Veronica Rezelj / Nick Hoppe / Morgane Boone / Christian B Billesbølle / Cristina Puchades / Caleigh M Azumaya / Huong T ...Authors: Michael Schoof / Bryan Faust / Reuben A Saunders / Smriti Sangwan / Veronica Rezelj / Nick Hoppe / Morgane Boone / Christian B Billesbølle / Cristina Puchades / Caleigh M Azumaya / Huong T Kratochvil / Marcell Zimanyi / Ishan Deshpande / Jiahao Liang / Sasha Dickinson / Henry C Nguyen / Cynthia M Chio / Gregory E Merz / Michael C Thompson / Devan Diwanji / Kaitlin Schaefer / Aditya A Anand / Niv Dobzinski / Beth Shoshana Zha / Camille R Simoneau / Kristoffer Leon / Kris M White / Un Seng Chio / Meghna Gupta / Mingliang Jin / Fei Li / Yanxin Liu / Kaihua Zhang / David Bulkley / Ming Sun / Amber M Smith / Alexandrea N Rizo / Frank Moss / Axel F Brilot / Sergei Pourmal / Raphael Trenker / Thomas Pospiech / Sayan Gupta / Benjamin Barsi-Rhyne / Vladislav Belyy / Andrew W Barile-Hill / Silke Nock / Yuwei Liu / Nevan J Krogan / Corie Y Ralston / Danielle L Swaney / Adolfo García-Sastre / Melanie Ott / Marco Vignuzzi / / Peter Walter / Aashish Manglik / Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kkj.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kkj.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kkj_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 7kkj_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 7kkj_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7kkj_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/7kkj ftp://data.pdbj.org/pub/pdb/validation_reports/kk/7kkj | HTTPS FTP |
-Related structure data
Related structure data | 7kkkC 7kklC 5vnvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 13641.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 1.0 M Aammonium sulfate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 2, 2020 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.105 Å / Num. obs: 16591 / % possible obs: 97.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.05 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1582 / Rpim(I) all: 0.39 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5VNV Resolution: 2.05→42.105 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 93.5 Å2 / Biso mean: 36.1272 Å2 / Biso min: 18.9 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→42.105 Å
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