RCSB PDB - 7L2E: Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein (original) (raw)
7L2E | pdb_00007l2e
Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein
This is version 1.3 of the entry. See complete history.
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
[Cerutti, G.](/search?q=citation.rcsb%5Fauthors:Cerutti, G.), [Guo, Y.](/search?q=citation.rcsb%5Fauthors:Guo, Y.), [Zhou, T.](/search?q=citation.rcsb%5Fauthors:Zhou, T.), [Gorman, J.](/search?q=citation.rcsb%5Fauthors:Gorman, J.), [Lee, M.](/search?q=citation.rcsb%5Fauthors:Lee, M.), [Rapp, M.](/search?q=citation.rcsb%5Fauthors:Rapp, M.), [Reddem, E.R.](/search?q=citation.rcsb%5Fauthors:Reddem, E.R.), [Yu, J.](/search?q=citation.rcsb%5Fauthors:Yu, J.), [Bahna, F.](/search?q=citation.rcsb%5Fauthors:Bahna, F.), [Bimela, J.](/search?q=citation.rcsb%5Fauthors:Bimela, J.), [Huang, Y.](/search?q=citation.rcsb%5Fauthors:Huang, Y.), [Katsamba, P.S.](/search?q=citation.rcsb%5Fauthors:Katsamba, P.S.), [Liu, L.](/search?q=citation.rcsb%5Fauthors:Liu, L.), [Nair, M.S.](/search?q=citation.rcsb%5Fauthors:Nair, M.S.), [Rawi, R.](/search?q=citation.rcsb%5Fauthors:Rawi, R.), [Olia, A.S.](/search?q=citation.rcsb%5Fauthors:Olia, A.S.), [Wang, P.](/search?q=citation.rcsb%5Fauthors:Wang, P.), [Zhang, B.](/search?q=citation.rcsb%5Fauthors:Zhang, B.), [Chuang, G.Y.](/search?q=citation.rcsb%5Fauthors:Chuang, G.Y.), [Ho, D.D.](/search?q=citation.rcsb%5Fauthors:Ho, D.D.), [Sheng, Z.](/search?q=citation.rcsb%5Fauthors:Sheng, Z.), [Kwong, P.D.](/search?q=citation.rcsb%5Fauthors:Kwong, P.D.), [Shapiro, L.](/search?q=citation.rcsb%5Fauthors:Shapiro, L.)
(2021) Cell Host Microbe 29: 819
PubMed Abstract:
Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.
Organizational Affiliation:
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: pdkwong@nih.gov.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA. Electronic address: lss8@columbia.edu.
Macromolecule Content
- Total Structure Weight: 586.62 kDa
- Atom Count: 32,641
- Modeled Residue Count: 4,050
- Deposited Residue Count: 5,196
- Unique protein chains: 3
| Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a],BA [auth b],CA [auth c],DA [auth d],EA [auth e],AA [auth a],BA [auth b],CA [auth c],DA [auth d],EA [auth e],FA [auth f],GA [auth g],J [auth D],K [auth E],L [auth F],M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z | 2 |  |
N-Glycosylation | Interactions Interactions & Density |
| Glycosylation Resources | |||||
| GlyTouCan: G42666HTGlyCosmos: G42666HTGlyGen: G42666HT |
| Ligands 1 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| NAG (Subject of Investigation/LOI)Query on NAG Download:Ideal Coordinates CCD File | AB [auth B]BB [auth C]CB [auth C]DB [auth C]EB [auth C]AB [auth B],BB [auth C],CB [auth C],DB [auth C],EB [auth C],FB [auth C],GB [auth C],HA [auth A],HB [auth C],IA [auth A],IB [auth C],JA [auth A],JB [auth C],KA [auth A],KB [auth C],LA [auth A],MA [auth A],NA [auth A],OA [auth A],PA [auth A],QA [auth A],RA [auth B],SA [auth B],TA [auth B],UA [auth B],VA [auth B],WA [auth B],XA [auth B],YA [auth B],ZA [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O6OVRNDRQMDRJTHS-FMDGEEDCSA-N |  |
Interactions Interactions & Density |
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.97 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
EM Software:
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC |
Deposition Data
- Released Date: 2021-03-24 Deposition Author(s): [Cerutti, G.](/search?q=audit%5Fauthor.name:Cerutti, G.), [Shapiro, L.](/search?q=audit%5Fauthor.name:Shapiro, L.)
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | China | Jack Ma Foundation |
Revision History (Full details and data files)
- Version 1.0: 2021-03-24
Type: Initial release - Version 1.1: 2021-04-14
Changes: Database references - Version 1.2: 2021-05-26
Changes: Database references - Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary