9E21 | pdb_00009e21

CryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody 52


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Germinal center-mediated broadening of B cell responses to SARS-CoV-2 booster immunization.

Malladi, S.K.Jaiswal, D.Ying, B.Alsoussi, W.B.Darling, T.L.Dadonaite, B.Civljak, A.Horvath, S.C.Zhou, J.Q.Kim, W.Turner, J.S.Schmitz, A.J.Han, F.Scheaffer, S.M.Farnsworth, C.W.Nachbagauer, R.Nestorova, B.Chalkias, S.Klebert, M.K.Edwards, D.K.Paris, R.Strnad, B.S.Middleton, W.D.O'Halloran, J.A.Presti, R.M.Bloom, J.D.Boon, A.C.M.Diamond, M.S.Bajic, G.Ellebedy, A.H.

(2025) Sci Immunol 10: eadu4107-eadu4107

  • DOI: https://doi.org/10.1126/sciimmunol.adu4107
  • Primary Citation of Related Structures:  
    9E21

  • PubMed Abstract: 

    Germinal centers (GCs) are key sites for antibody diversification and affinity maturation. SARS-CoV-2 messenger RNA (mRNA) vaccines elicit robust GC B cell responses in humans, but how these responses influence the breadth of immunity against viral variants remains unclear. We analyzed GC B cell responses in nine healthy adults after mRNA booster immunization. We show that 77.8% of the B cell clones in the GC expressed representative monoclonal antibodies (mAbs) recognizing the spike protein, with 37.8% of these targeting the receptor binding domain (RBD). One RBD-targeting mAb, mAb-52, neutralized all tested SARS-CoV-2 strains, including the recent XEC variant. mAb-52 used the IGHV3-66 public clonotype, protected hamsters challenged against the EG.5.1 variant, and targeted the class I/II RBD epitope, closely mimicking the binding footprint of ACE2. Its broad reactivity was driven by extensive somatic hypermutation, underscoring the critical role of GC reactions in shaping cross-variant B cell immunity after SARS-CoV-2 booster vaccination.


  • Organizational Affiliation
    • Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
52 Fab Heavy chainA [auth H]117Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
52 Fab light chainB [auth L]106Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SARS XBB.1.5 SpikeC [auth S]201Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for A0A6V7ALX9 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A6V7ALX9 
Go to UniProtKB:  A0A6V7ALX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6V7ALX9
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI168178

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Data collection, Database references