7LM9 | pdb_00007lm9

Crystal structure of SARS-CoV spike protein receptor-binding domain in complex with a cross-neutralizing antibody CV38-142 Fab isolated from COVID-19 patient

• PDB DOI: https://doi.org/10.2210/pdb7LM9/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): SARS coronavirus MA15, Homo sapiens
• Expression System: Trichoplusia ni, Mus musculus
• Mutation(s): No 


• Deposited: 2021-02-05 Released: 2021-03-31 
• Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Models: experimental

Literature

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.

Liu, H., Yuan, M., Huang, D., Bangaru, S., Zhao, F., Lee, C.D., Peng, L., Barman, S., Zhu, X., Nemazee, D., Burton, D.R., van Gils, M.J., Sanders, R.W., Kornau, H.C., Reincke, S.M., Pruss, H., Kreye, J., Wu, N.C., Ward, A.B., Wilson, I.A.

(2021) Cell Host Microbe 29: 806-818.e6

• PubMed: 33894127 
• DOI: https://doi.org/10.1016/j.chom.2021.04.005
• Primary Citation Related Structures: 
  7LM8, 7LM9


• PubMed Abstract: 
  

  Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.
German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany.
German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany.
German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.15 kDa 
• Atom Count: 5,619 
• Modeled Residue Count: 634 
• Deposited Residue Count: 673 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	230	SARS coronavirus MA15	Mutation(s): 0
UniProt
Find proteins for D2E265 (SARS coronavirus MA15) Explore D2E265  Go to UniProtKB:  D2E265
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CV38-142 Fab heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CV38-142 Fab light chain	C [auth L]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth H], J [auth H], K [auth L], L, M [auth L], N [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237.997	α = 90
b = 71.877	β = 90.78
c = 49.241	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
Bill & Melinda Gates Foundation	United States	INV-004923

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary