11HM | pdb_000011hm

1332D4-RBD KP3.1.1 Complex

• PDB DOI: https://doi.org/10.2210/pdb11HM/pdb
• EM Map EMD-75696: EMDB EMDataResource

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


• Deposited: 2026-02-24 Released: 2026-08-26 
• Deposition Author(s): Kizziah, J.L., Walter, M.R.
• 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: 3.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Emergence of neutralizing RBD antibodies following Omicron infection with limited activity against ancestral SARS-CoV-2.

Piepenbrink, M.S., Ma, Y., Panjwani, S., Blake, A.R., Bell, A.M., Kizziah, J.L., Mahmoud, S.H., Ippolito, G.C., Erdmann, N.B., Goepfert, P.A., Martinez-Sobrido, L., Kobie, J.J., Walter, M.R.

(2026) iScience 29: 117166-117166

• PubMed: 42621159 
• DOI: https://doi.org/10.1016/j.isci.2026.117166
• Primary Citation Related Structures: 
  11HM, 11HO, 11IS, 11IT


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution reduces the efficacy of prophylactic vaccines and monoclonal antibody (mAb) therapies. To evaluate potency and breadth, receptor binding domain (RBD)-targeting neutralizing mAbs were identified from patient B cells using an Omicron KP3.1.1 Spike (S) protein bait. MAbs exhibiting the greatest neutralization potency (1332D4 and 1332E5) and binding breadth (1324A10 and 1316C10) were evaluated in greater detail. Cryo-electron microscopy (Cryo-EM) studies revealed 1332D4 and 1332E5 target RBD residue segments 439-446 and 498-506 of KP3.1.1 S, respectively. 1332E5 is a knob ^498-506 -targeting class-1/4 mAb that exhibits pan-Omicron specificity but does not bind or neutralize ancestral Wuhan-1. Further analysis suggests mAbs generically defined as class 1/4 mAbs may be separated into two classes. Class 1/4 mAbs, like 1332E5, and class 4/1 mAbs that make extensive interactions with the class-4 epitope and limited contacts with the class-1 knob ^498-596 . Despite these differences, the specificity of both mAb classes can be altered by mutations in knob ^498-506 .

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Organizational Affiliation: 
• Heersink School of Medicine, Infectious Diseases Division, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Department of Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
Heersink School of Medicine, Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 191.46 kDa 
• Atom Count: 3,300 
• Modeled Residue Count: 413 
• Deposited Residue Count: 1,732 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 KP3.1.1	A [auth B]	1,258	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1332D4 Heavy Chain	B [auth D]	240	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1332D4 Light Chain	C [auth E]	234	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth B], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	v4.5.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Kizziah, J.L., Walter, M.R.

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

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release
  
• Version 1.1: 2026-09-02
  Changes: Data collection, Database references