9PSP | pdb_00009psp

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.247 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.

Fu, Y.Feng, Z.Erickson, S.A.Halfmann, P.J.Li, L.Chervin, J.C.Troxell, C.A.Sun, J.Yasuhara, A.Changrob, S.Huang, M.Zheng, N.Y.Yuan, M.Kawaoka, Y.Wilson, I.A.Wilson, P.C.

(2026) Cell Rep 45: 117137-117137

  • DOI: https://doi.org/10.1016/j.celrep.2026.117137
  • Primary Citation Related Structures: 
    9PSN, 9PSO, 9PSP

  • PubMed Abstract: 

    The epitope that monoclonal CR3022 binds to represents a promising target for broad protection against a wide range of human and zoonotic coronaviruses. We develop a powerful model to evaluate antibody affinity maturation in vivo using immunoglobulin (Ig)-humanized mice that express the predicted germline heavy chain of antibody CR3022. Severe acute respiratory syndrome coronavirus (SARS-CoV)/SARS-CoV-2 sequential immunization leads to the convergent evolution of the germline CR3022 through somatic hypermutation (SHM), resembling the affinity-matured CR3022 from a human but now also adapting to key variants and divergent sarbecoviruses. While simple prime-boost strategies drive CR3022-epitope targeting, an intensive vaccination protocol elicits dominant responses to other epitopes. X-ray crystal structures reveal that SARS-CoV-2-neutralizing CR3022-like antibodies exhibit enhanced affinity by increasing polar and electrostatic interactions. Overall, these findings show that CR3022-like clones can be readily adapted through SHM to increase breadth and potency to sarbecoviruses by relatively minor shifts in affinity with appropriate vaccination strategies.


  • Organizational Affiliation
    • Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 237.95 kDa 
  • Atom Count: 16,598 
  • Modeled Residue Count: 2,117 
  • Deposited Residue Count: 2,172 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1 receptor binding domainA [auth T],
B [auth U]
209Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CC12.3 Fab heavy chainC [auth K],
E [auth M]
220Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CC12.3 Fab light chainD [auth W],
F [auth N]
215Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BoWLB-1173 Fab heavy chainG [auth H],
I [auth A]
221Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
BoWLB-1173 Fab light chainH [auth L],
J [auth B]
221Mus musculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth V]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
T [auth H]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth T]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
S [auth N],
U [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
M [auth U],
N [auth K],
O [auth K],
P [auth K],
Q [auth W]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
R [auth W]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.247 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.195α = 92.25
b = 101.051β = 100.66
c = 127.826γ = 90.09
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI190286

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references