9OA9 | pdb_00009oa9

CryoEM structure of anti-MHC-I mAb B1.23.2 Fc domains

• PDB DOI: https://doi.org/10.2210/pdb9OA9/pdb
• EM Map EMD-70276: EMDB EMDataResource

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-04-20 Released: 2026-02-04 
• Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H.
• 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: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

CryoEM structure of anti-MHC-I B1.23.2 Fc domains

Jiang, J., Natarajan, K., Margulies, D.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 99.24 kDa 
• Atom Count: 3,676 
• Modeled Residue Count: 550 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-MHC-I mAb B1.23.2 Fc domains H-chain	A [auth J], B [auth K]	443	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth X]	6		N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth Y]	6		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H.

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

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release