9M5B | pdb_00009m5b

A Human Fc Receptor Ectodomain in Complex With a Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chimeras co-targeting antigens and Fc gamma RIIb trigger degradation of extracellular soluble proteins and pathological aggregates.

Du, M.Li, N.Li, T.Zhao, Z.Liu, H.Li, X.Gong, N.Duan, B.Wang, W.Jian, Y.Ma, W.Zhang, X.Wang, Y.Zhang, Z.Bai, Y.Wang, X.Wang, C.Liu, J.Guan, X.Zhou, F.Wang, W.Li, L.Zhu, X.Lei, Y.Duan, Y.Han, G.Wei, P.Gao, S.Wang, S.Chen, A.Huang, Y.Yang, H.Xue, X.Zhang, H.

(2025) Nat Commun 17: 514-514

  • DOI: https://doi.org/10.1038/s41467-025-67207-4
  • Primary Citation of Related Structures:  
    9M5B

  • PubMed Abstract: 

    While the clinical utility of conventional antibody therapies is undeniable, their therapeutic potential is often constrained high antigen loads and the recycling of antibody-antigen complexes via neonatal Fc receptor (FcRn). Here, we present a platform, based on a design similar to bispecific antibodies, FcγRIIb-Targeting Chimeras (FcRTAC). These constructs recognise antigens with one arm and bind FcγRIIb with the other arm to harness the unique endocytic properties of FcγRIIb to direct the recognized pathogenic antigens to lysosomes for irreversible degradation. The FcRTAC platform demonstrates broad therapeutic potential across multiple disease-relevant targets, including IgE, proprotein convertase subtilisin/kexin type 9 (PCSK9) and amyloid-β (Aβ). Notably, a single intravenous administration of blood brain barrier (BBB)-penetrating adeno-associated viral vector (AAV) encoding an Aβ-targeting FcRTAC construct achieves sustained therapeutic effects, establishing proof-of-concept for AAV-mediated delivery of an Aβ degrader as a strategy for Alzheimer's disease treatment. Our comprehensive investigation of binding properties of FcRTACs reveals critical molecular determinants of function and enables development of optimized engineering approaches. In summary, our approach represents a versatile therapeutic platform for treating diverse diseases ranging from autoimmune disorders to neurodegenerative conditions, while simultaneously serving as a user-friendly, plug-and-play research tool for extracellular protein knockout in basic biological research.


  • Organizational Affiliation
    • Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin gamma Fc region receptor II-bA [auth C]206Homo sapiensMutation(s): 0 
Gene Names: FCGR2BCD32FCG2IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P31994 (Homo sapiens)
Explore P31994 
Go to UniProtKB:  P31994
PHAROS:  P31994
GTEx:  ENSG00000072694 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31994
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainC [auth A]230Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.637α = 90
b = 83.36β = 109.97
c = 68.588γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82261138553
National Natural Science Foundation of China (NSFC)China82373898

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references
  • Version 1.2: 2026-01-28
    Changes: Database references