9CPY | pdb_00009cpy

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Literature

In vivo antibody diversification targeting a conserved coronavirus epitope.

Nair, U.Feng, Z.Akauliya, M.Esposito, A.G.Crain, C.R.Lamperti, E.D.Prum, T.Warner, J.E.Madungwe, L.Dale, G.A.Boucau, J.Gaiha, G.D.Yuan, M.Wilson, I.A.Batista, F.D.

(2025) J Exp Medicine 222

  • DOI: https://doi.org/10.1084/jem.20241563
  • Primary Citation of Related Structures:  
    9CPP, 9CPQ, 9CPR, 9CPS, 9CPT, 9CPU, 9CPV, 9CPW, 9CPX, 9CPY

  • PubMed Abstract: 

    To explore the use of human B cell receptor (BCR) knock-in mice for broadening antibody responses, we diversified CR3022, a monoclonal antibody (mAb) originally identified in a 2003 severe acute respiratory syndrome coronavirus (SARS-CoV) convalescent patient. This mAb targets a conserved epitope on the coronavirus receptor-binding domain (RBD). We took advantage of high- and low-affinity CR3022 BCR knock-in mice and immunized them with SARS-CoV-2 Wuhan RBD trimers to expand the breadth of these antibodies toward this virus. The resulting antibodies retained the ability to neutralize SARS-CoV and exhibited enhanced affinity and neutralization against the SARS-CoV-2 WA1/2020 strain, as well as the Delta (B.1.617.2) and Omicron KP.3 variants. They also showed broadened reactivity to two bat coronaviruses: WIV1 and, to a lesser potency, BtKY72. Structural analysis revealed key mutations that enhanced binding and neutralization, highlighting the importance of epitope accessibility and variant-specific conformations in antibody diversification. These findings demonstrate that human BCR-expressing mouse models can generate effective antibodies with broad neutralizing activity against viral epitopes.


  • Organizational Affiliation
    • The Ragon Institute of Mass General, MIT, and Harvard , Cambridge, MA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C11-0860 Fab heavy chainA [auth H]222Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C11-0860 Fab light chainB [auth L]220Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CC12.3 Fab heavy chain220Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CC12.3 Fab light chain214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1E [auth A]205Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.245α = 90
b = 109.245β = 90
c = 229.199γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references