9C6Y | pdb_00009c6y

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 
    0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.

Zost, S.J.Suryadevara, N.Williamson, L.E.Scheaffer, S.M.Binshtein, E.Buchman, C.D.Johnson, N.V.Catanzaro, N.J.Ravera, S.Chapman, N.S.Myers, L.Ramamohan, A.R.Handal, L.S.Nguyen, D.C.Trivette, A.Martinez, J.R.Villalobos, E.Rutherford, S.A.Eun-Hyung Lee, F.Schafer, A.Baric, R.S.McLellan, J.S.Diamond, M.S.Carnahan, R.H.Crowe Jr., J.E.

(2026) Nat Microbiol 

  • DOI: https://doi.org/10.1038/s41564-026-02282-x
  • Primary Citation Related Structures: 
    9C6Y

  • PubMed Abstract: 

    The emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co-circulation of SARS-CoV-2 variants with unique sets of antigenic substitutions has further complicated therapeutic mAb discovery. New approaches are needed to rapidly discover and characterize mAbs with preferred specificity and functional characteristics. Here we describe and perform epitope-focused mAb discovery using glycan-masked antigens. We isolated and expressed a panel of 303 mAbs, some of which potently neutralize divergent Omicron subvariants by targeting the class 3 antigenic site on SARS-CoV-2 RBD. Epitope mapping of these antibodies revealed a spectrum of cross-reactivity and differential recognition of the class 3 site, validating the utility of this enrichment approach for targeted mAb discovery. Together, this work rationally designs glycan-masked engineered RBDs and uses them to isolate mAbs that potently neutralize antigenically divergent SARS-CoV-2 variants.


  • Organizational Affiliation
    • The Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of COV2-3906 Fab
A, C
225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of COV2-3906 Fab
B, D
216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S2'
E, F
216Severe acute respiratory syndrome coronavirusMutation(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: 3Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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
G
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-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
H
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00395TQ
GlyCosmos:  G00395TQ
GlyGen:  G00395TQ
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
N [auth E],
R [auth F]
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth E],
Q [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
O [auth E],
P [auth E],
S [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.971α = 90
b = 170.851β = 90
c = 231.543γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Defense Advanced Research Projects Agency (DARPA)United StatesHR0011-18-2-0001
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI157155

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references