Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 45.38 kDa 
• Atom Count: 3,192 
• Modelled Residue Count: 406 
• Deposited Residue Count: 406 
• Unique protein chains: 3

 7MKM

SARS-CoV-2 Spike RBD in complex with neutralizing Fab SARS2-38 (local refinement)

• PDB DOI:  https://doi.org/10.2210/pdb7MKM/pdb
• EM Map EMD-23899: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-04-24 Released: 2021-05-12 
• Deposition Author(s): Adams, L.J., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope.

VanBlargan, L.A., Adams, L.J., Liu, Z., Chen, R.E., Gilchuk, P., Raju, S., Smith, B.K., Zhao, H., Case, J.B., Winkler, E.S., Whitener, B.M., Droit, L., Aziati, I.D., Bricker, T.L., Joshi, A., Shi, P.Y., Creanga, A., Pegu, A., Handley, S.A., Wang, D., Boon, A.C.M., Crowe Jr., J.E., Whelan, S.P.J., Fremont, D.H., Diamond, M.S.

(2021) Immunity 54: 2399-2416.e6

• PubMed: 34481543 
• DOI: https://doi.org/10.1016/j.immuni.2021.08.016
• Primary Citation of Related Structures:  
  7MKL, 7MKM


• PubMed Abstract: 
  

With the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here, we developed a panel of neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) that bound the receptor binding domain of the spike protein at distinct epitopes and blocked virus attachment to its host receptor, human angiotensin converting enzyme-2 (hACE2). Although several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by ancestral SARS-CoV-2 strains, others induced escape variants in vivo or lost neutralizing activity against emerging strains. One mAb, SARS2-38, potently neutralized all tested SARS-CoV-2 variants of concern and protected mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engaged a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of neutralizing antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.

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Related Citations: 

• A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope.
  VanBlargan, L., Adams, L., Liu, Z., Chen, R.E., Gilchuk, P., Raju, S., Smith, B., Zhao, H., Case, J.B., Winkler, E.S., Whitener, B., Droit, L., Aziati, I., Shi, P.Y., Creanga, A., Pegu, A., Handley, S., Wang, D., Boon, A., Crowe, J.E., Whelan, S.P.J., Fremont, D., Diamond, M.
  (2021) Biorxiv --: --

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Organizational Affiliation: 

Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	188	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS2-38 Fv heavy chain	B [auth H]	113	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS2-38 Fv light chain	C [auth L]	105	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.1.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Adams, L.J., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93019C00062
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 2.0: 2021-08-04
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2021-12-01
  Changes: Database references