13BD | pdb_000013bd

Local refinement of the RBD and NTD in the closed BA.3.2.1 spike with N529Q mutant

• PDB DOI: https://doi.org/10.2210/pdb13BD/pdb
• EM Map EMD-76936: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-04-27 Released: 2026-06-17 
• Deposition Author(s): Wang, Y., Hu, Y., Xie, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Functional and structural basis of Omicron BA.3.2.1 spike.

Wang, Y., Hu, Y., Chen, Z., Zou, J., Zhang, K., Ren, P., Shi, P.Y., Liang, B., Xie, X.

(2026) Cell Rep 45: 117812-117812

• PubMed: 42571698 
• DOI: https://doi.org/10.1016/j.celrep.2026.117812
• Primary Citation Related Structures: 
  12JT, 12JZ, 12RP, 13BD


• PubMed Abstract: 
  

  SARS-CoV-2 BA.3.2 sublineages, derived from BA.3 and carrying substantial spike divergence, raised concerns about altered fitness and antigenicity. Using BA.3.2.1 as a representative strain, we engineered live-attenuated SARS-CoV-2 encoding BA.3.2.1, LP.8.1, or XEC spikes and benchmarked them against BA.3 and KP.3. BA.3.2.1 outcompetes BA.3 in primary human airway epithelium but replicates less efficiently than JN.1 descendants and shows the greatest resistance to neutralization by KP.2/KP.3 convalescent sera. Although BA.3.2.1 RBD binds hACE2 with high affinity, its trimeric spike engages hACE2 less efficiently than LP.8.1. Cryoelectron microscopy structures reveal that BA.3.2.1 spike predominantly adopts a compact, asymmetric closed conformation stabilized by protomer rearrangements, N-linked glycosylation, and a distinct fusion-peptide-proximal region. This architecture increases spike stability, limits receptor engagement, reduces fusogenicity, and masks antibody-sensitive epitopes. Thus, BA.3.2.1 enhances immune evasion at the cost of replication fitness, providing a structural-functional explanation for BA.3.2's limited prevalence and underscoring the need for continued variant surveillance.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 284.25 kDa 
• Atom Count: 3,825 
• Modeled Residue Count: 461 
• Deposited Residue Count: 2,542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.3.2.2 Spike with N529Q mutation	A [auth C], B [auth A]	1,271	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth C], E [auth C], F [auth C], G [auth C], H [auth C], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Wang, Y., Hu, Y., Xie, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release
  
• Version 1.1: 2026-08-19
  Changes: Data collection, Database references