9MKG | pdb_00009mkg

Cryo-EM structure of human CD33 bound to 15G15.3 Fab

• PDB DOI: https://doi.org/10.2210/pdb9MKG/pdb
• EM Map EMD-48326: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-17 Released: 2026-06-24 
• Deposition Author(s): Puno, M.R., Azumaya, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Rational design of oxidation-resistant antibodies through local electrostatic modulation

Lenka, S., Stephens, N., Mehta, S., Seeger, F., Jafari, N., Liang, W.C., Watkins, A., Kelly, R., Wu, S., Puno, M.R., Azumaya, C., Irudayanathan, J., Zarzar, J., Alavattam, S., Kelley, B., Izadi, S.

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)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 78.32 kDa 
• Atom Count: 4,262 
• Modeled Residue Count: 553 
• Deposited Residue Count: 718 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
15G15.3 Fab heavy chain	A	222	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15G15.3 Fab light chain	B	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid cell surface antigen CD33	C	277	Homo sapiens	Mutation(s): 0  Gene Names: CD33, SIGLEC3
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens) Explore P20138  Go to UniProtKB:  P20138
PHAROS:  P20138 GTEx:  ENSG00000105383

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5015:
RECONSTRUCTION	cryoSPARC	4.3.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Puno, M.R., Azumaya, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release