9VL2 | pdb_00009vl2

Structure of CD33 complexed with its mAb-10C8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: in silico
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Literature

Crystal structure of the CD33/Fab-10C8 complex elucidates the mechanism of antibody antagonism in HBV-induced immunosuppression.

Yeh, Y.H.Lin, M.G.Sung, P.S.Hsieh, S.L.Hsiao, C.D.

(2026) J Biomed Sci 33

  • DOI: https://doi.org/10.1186/s12929-026-01248-9
  • Primary Citation Related Structures: 
    9VL2

  • PubMed Abstract: 

    Hepatitis B virus (HBV) infection persists through immune evasion strategies, including engagement of the inhibitory receptor CD33 (Siglec-3) by α2,6-linked sialoglycans on HBsAg. This interaction induces ITIM phosphorylation and SHP-1/2 recruitment, dampening myeloid cell activation. The monoclonal antibody 10C8 has been identified as a potent antagonist of CD33, but the structural basis for its inhibitory activity remains unclear. We determined the 3.2 Å crystal structure of the human CD33 extracellular domain (CD33-ECD) in complex with the Fab fragment of 10C8 (Fab-10C8). The stoichiometry and assembly of the complex in solution were validated by size-exclusion chromatography and analytical ultracentrifugation (AUC). Structural comparisons with apo CD33 were performed to assess potential Fab-induced conformational changes, and buried surface area analyses were conducted to characterize binding interfaces. The structure reveals a 2:2 stoichiometry complex comprising two CD33-ECD molecules and two Fab-10C8 fragments, consistent with the 157 kDa molecular mass determined by AUC. Each Fab engages the V-set domain through extensive complementarity-determining region (CDR) interactions, burying ~612 Å 2 of surface area, while inter-Fab contacts stabilize a compact dimeric arrangement of CD33-ECD. This geometry differs markedly from the relaxed apo state, showing a ~21° reduction in the dimer angle. The antibody-binding epitope is adjacent to, but not overlapping with, the canonical sialic acid-binding cleft, leading to steric occlusion that prevents HBsAg engagement. Together with a potential Fab-induced ectodomain compaction, this conformation restricts CD33 clustering and likely precludes SHP-1/2 recruitment, providing a mechanistic explanation for the antagonistic activity of 10C8. This study provides the structural insight into antibody-mediated inhibition of CD33. By locking CD33 into a sterically occluded, signaling-refractory conformation, 10C8 effectively reverses HBV-induced immunosuppression, thereby restoring host antiviral activity. These findings establish a structural framework for rational design of Siglec-targeted immunotherapies against chronic viral infections and other immune regulatory disorders.


  • Organizational Affiliation
    • Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 142.85 kDa 
  • Atom Count: 9,952 
  • Modeled Residue Count: 1,282 
  • Deposited Residue Count: 1,294 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myeloid cell surface antigen CD33
A, D
214Homo sapiensMutation(s): 0 
Gene Names: CD33SIGLEC3
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
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P20138-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
light chain of Fab-10C8
B, E
213Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
heavy chain of Fab-10C8
C, F
220Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.408α = 95.89
b = 71.156β = 94.16
c = 86.765γ = 111.23
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Database references