9BET | pdb_00009bet

Structure of the human CD33 transmembrane domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 21 
  • Conformers Submitted: 21 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the CD33 Receptor and Implications for the Siglec Family.

Vu, H.N.Situ, A.J.Dai, X.Ulmer, T.S.

(2025) Biochemistry 64: 1450-1462

  • DOI: https://doi.org/10.1021/acs.biochem.4c00864
  • Primary Citation of Related Structures:  
    9BET

  • PubMed Abstract: 

    In the innate immune system, the CD33 receptor modulates microglial activity. Its downregulation promises to slow Alzheimer's disease, and it is already targeted in blood cancers. The mechanism underlying CD33 signaling is unresolved. Starting from the available crystal structure of its extracellular IgV-IgC1 domains, we have assembled a model of the human CD33 receptor by characterizing the oligomerization and structure of IgC1, transmembrane, and cytosolic domains in solution. IgC1 homodimerizes via intermolecular β-strand pairing and packing. In contrast, the 21-residue transmembrane helix of CD33 appears monomeric and straight, with a conserved thin neck and thick belly appearance followed by a positively charged cytosolic patch. The cytosolic domain is dynamically unstructured. Sequence alignment and AlphaFold models indicate that IgC domains in the family of human Siglecs, to which CD33 belongs, are surprisingly variable. Only Siglec-6 is identified to analogously dimerize via IgC1. Our CD33 structural model suggests that the receptor is not signaling via a monomer-dimer shift. Rather, we propose that, aided but also constrained by dimerization, multivalent ligands may concentrate the receptor transmembrane and cytosolic domains sufficiently to trigger colocalization with an activating kinase.


  • Organizational Affiliation
    • Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid cell surface antigen CD3342Homo sapiensMutation(s): 0 
Gene Names: CD33SIGLEC3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens)
Explore P20138 
Go to UniProtKB:  P20138
PHAROS:  P20138
GTEx:  ENSG00000105383 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20138
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 21 
  • Conformers Submitted: 21 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01AG072442

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references