7MM0 | pdb_00007mm0

Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain

• PDB DOI: https://doi.org/10.2210/pdb7MM0/pdb
• EM Map EMD-23915: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-04-29 Released: 2021-07-28 
• Deposition Author(s): Zhou, T., Tsybovsky, T., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants.

Wang, L., Zhou, T., Zhang, Y., Yang, E.S., Schramm, C.A., Shi, W., Pegu, A., Oloniniyi, O.K., Henry, A.R., Darko, S., Narpala, S.R., Hatcher, C., Martinez, D.R., Tsybovsky, Y., Phung, E., Abiona, O.M., Antia, A., Cale, E.M., Chang, L.A., Choe, M., Corbett, K.S., Davis, R.L., DiPiazza, A.T., Gordon, I.J., Hait, S.H., Hermanus, T., Kgagudi, P., Laboune, F., Leung, K., Liu, T., Mason, R.D., Nazzari, A.F., Novik, L., O'Connell, S., O'Dell, S., Olia, A.S., Schmidt, S.D., Stephens, T., Stringham, C.D., Talana, C.A., Teng, I.T., Wagner, D.A., Widge, A.T., Zhang, B., Roederer, M., Ledgerwood, J.E., Ruckwardt, T.J., Gaudinski, M.R., Moore, P.L., Doria-Rose, N.A., Baric, R.S., Graham, B.S., McDermott, A.B., Douek, D.C., Kwong, P.D., Mascola, J.R., Sullivan, N.J., Misasi, J.

(2021) Science 373

• PubMed: 34210892 
• DOI: https://doi.org/10.1126/science.abh1766
• Primary Citation Related Structures: 
  7LRS, 7LRT, 7MLZ, 7MM0


• PubMed Abstract: 
  

  The emergence of highly transmissible SARS-CoV-2 variants of concern (VOCs) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identified four receptor binding domain-targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 23 variants, including the B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, and B.1.617 VOCs. Two antibodies are ultrapotent, with subnanomolar neutralization titers [half-maximal inhibitory concentration (IC ₅₀ ) 0.3 to 11.1 nanograms per milliliter; IC ₈₀ 1.5 to 34.5 nanograms per milliliter). We define the structural and functional determinants of binding for all four VOC-targeting antibodies and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting their potential in mitigating resistance development.

---

Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 456.9 kDa 
• Atom Count: 28,057 
• Modeled Residue Count: 3,490 
• Deposited Residue Count: 4,028 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B1-182.1 Fab heavy chain	A [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B1-182.1 Fab light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A], D [auth B], E [auth C]	1,195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 15		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

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	F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M, N, P, Q, R, S	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], T [auth A], TA [auth C], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Zhou, T., Tsybovsky, T., Kwong, P.D.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Intramural

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2021-08-11
  Changes: Database references
• Version 1.3: 2021-08-25
  Changes: Database references
• Version 1.4: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary