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

• DOI: https://doi.org/10.1016/j.isci.2026.117166

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