|Entry||Database: EMDB / ID: EMD-22908|
|Title||SARS-CoV-2 Spike bound to Nb6 in open conformation|
|Sample||Complex of Spike S2P glycoprotein with synthetic nanobody Nb6:|
Spike S2P glycoprotein / synthetic nanobody Nb6
|Biological species||Severe acute respiratory syndrome coronavirus 2 / synthetic construct (others)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.8 Å|
|Authors||Schoof MS / Faust BF / Saunders RA / Sangwan S / Rezelj V / Hoppe N / Boone M / Billesboelle CB / Puchades C / Azumaya CM ...Schoof MS / Faust BF / Saunders RA / Sangwan S / Rezelj V / Hoppe N / Boone M / Billesboelle CB / Puchades C / Azumaya CM / Kratochvil HT / Zimanyi M / Desphande I / Liang J / Dickinson S / Nguyen HC / Chio CM / Merz GE / Thompson MC / Diwanji D / Schaefer K / Anand AA / Dobzinski N / Zha BS / Simoneau CR / Leon K / White KM / Chio US / Gupta M / Jin M / Li F / Liu Y / Zhang K / Bulkley D / Sun M / Smith AM / Rizo AN / Moss F / Brilot AF / Pourmal S / Trenker R / Pospiech T / Gupta S / Barsi-Rhyne B / Belyy V / Barile-Hill AW / Nock S / Liu Y / Krogan NJ / Ralston CY / Swaney DL / Garcia-Sastre A / Ott M / Vignuzzi M / Walter P / Manglik A / QCRG Structural Biology Consortium|
|Funding support|| United States, 1 items |
|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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22908.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.834 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Complex of Spike S2P glycoprotein with synthetic nanobody Nb6
|Entire||Name: Complex of Spike S2P glycoprotein with synthetic nanobody Nb6|
Number of components: 3
-Component #1: protein, Complex of Spike S2P glycoprotein with synthetic nanobody Nb6
|Protein||Name: Complex of Spike S2P glycoprotein with synthetic nanobody Nb6|
Recombinant expression: No
-Component #2: protein, Spike S2P glycoprotein
|Protein||Name: Spike S2P glycoprotein / Recombinant expression: No|
|Source||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Cricetulus griseus (Chinese hamster) / Cell of expression system: ExpiCHO|
-Component #3: protein, synthetic nanobody Nb6
|Protein||Name: synthetic nanobody Nb6 / Recombinant expression: No|
|Source||Species: synthetic construct (others)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 66 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Bioquantum|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image acquisition||Number of digital images: 5317|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 40125|
|3D reconstruction||Software: cisTEM|
CTF correction: Performed at reconstruction, as is standard for cryoSPARC
Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
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