9E21 | pdb_00009e21

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

• PDB DOI: https://doi.org/10.2210/pdb9E21/pdb
• EM Map EMD-47426: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-21 Released: 2025-07-30 
• Deposition Author(s): Jaiswal, D., Bajic, G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

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

Literature

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

Jaiswal, D., Bajic, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 46.68 kDa 
• Atom Count: 3,285 
• Modeled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
52 Fab Heavy chain	A [auth H]	117	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
52 Fab light chain	B [auth L]	106	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS XBB.1.5 Spike	C [auth S]	201	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A6V7ALX9 (Severe acute respiratory syndrome coronavirus 2) Explore A0A6V7ALX9  Go to UniProtKB:  A0A6V7ALX9
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Jaiswal, D., Bajic, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI168178

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release