29ZV | pdb_000029zv

Crystal structure of Fc heterodimer with StrandLock CH3 interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 29ZV

This is version 1.0 of the entry. See complete history

Literature

Engineering Fc heterodimerization via asymmetric beta-strand reconfiguration for bispecific antibody assembly.

Cano, A.Morillo, I.Goenaga, A.Laugieri, M.E.de Blas, A.Valdaliso-Diez, E.Ereno-Orbea, J.Apellaniz, B.Rujas, E.

(2026) J Biol Eng 

  • DOI: https://doi.org/10.1186/s13036-026-00717-x
  • Primary Citation Related Structures: 
    29ZV

  • PubMed Abstract: 

    Bispecific antibodies (bsAbs) have unlocked new therapeutic modalities by enabling dual antigen targeting, offering transformative potential in oncology and autoimmune diseases. However, the efficient production of full-length IgG-like bsAbs remains hindered by mispairing of heavy and light chains, yielding heterogeneous, low-purity products. Here, we present an Fc engineering strategy, termed StrandLock, that enables the controlled assembly of bsAbs through asymmetric β-strand redistribution at the CH3 dimer interface, in which the β-strand segment (residues N390-S400) is duplicated in one heavy chain and deleted from the partner. This structural asymmetry, combined with targeted point mutations, promotes obligate heterodimerization while suppressing homodimer formation. Importantly, these modifications enable the correct assembly of bsAbs with purities approaching 99% and allow streamlined manufacturing via a single-step affinity purification process comparable to that used for monoclonal antibodies. The engineered bsAbs retain key Fc effector functions and exhibit comparable in vivo pharmacokinetics to native IgG. Structural analysis confirms preservation of the CH3 fold and native-like interfacial packing. Despite a modest reduction in thermal stability, the molecules remain aggregation-resistant and functionally robust under accelerated stress conditions. We further demonstrate the versatility of the StrandLock design across multiple antibody pairs underscoring its utility as a strategy for bsAb production.


  • Organizational Affiliation
    • Department of Physiology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, 01006, Spain.

Macromolecule Content 

  • Total Structure Weight: 54.09 kDa 
  • Atom Count: 3,593 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 459 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fc_ChainBA [auth B]220Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fc_ChainAB [auth A]239Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
7N-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.639α = 90
b = 75.314β = 90
c = 148.553γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Worldwide Cancer ResearchUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release