8GV0

Crystal structure of anti-FIXa IgG fab without FAST-Ig mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Efficient production of bispecific antibody by FAST-Ig TM and its application to NXT007 for the treatment of hemophilia A.

Koga, H.Yamano, T.Betancur, J.Nagatomo, S.Ikeda, Y.Yamaguchi, K.Nabuchi, Y.Sato, K.Teranishi-Ikawa, Y.Sato, M.Hirayama, H.Hayasaka, A.Torizawa, T.Haraya, K.Sampei, Z.Shiraiwa, H.Kitazawa, T.Igawa, T.Kuramochi, T.

(2023) MAbs 15: 2222441-2222441

  • DOI: https://doi.org/10.1080/19420862.2023.2222441
  • Primary Citation of Related Structures:  
    8GUZ, 8GV0, 8GV1, 8GV2

  • PubMed Abstract: 

    Efficient production of bispecific antibodies (BsAbs) in single mammalian cells is essential for basic research and industrial manufacturing. However, preventing unwanted pairing of heavy chains (HCs) and light chains (LCs) is a challenging task. To address this, we created an engineering technology for preferential cognate HC/LC and HC/HC paring called FAST-Ig (Four-chain Assembly by electrostatic Steering Technology - Immunoglobulin), and applied it to NXT007, a BsAb for the treatment of hemophilia A. We introduced charged amino-acid substitutions at the HC/LC interface to facilitate the proper assembly for manufacturing a standard IgG-type BsAb. We generated CH1/CL interface-engineered antibody variants that achieved > 95% correct HC/LC pairing efficiency with favorable pharmacological properties and developability. Among these, we selected a design (C3) that allowed us to separate the mis-paired species with an unintended pharmacological profile using ion-exchange chromatography. Crystal structure analysis demonstrated that the C3 design did not affect the overall structure of both Fabs. To determine the final design for HCs-heterodimerization, we compared the stability of charge-based and knobs into hole-based Fc formats in acidic conditions and selected the more stable charge-based format. FAST-Ig was also applicable to stable CHO cell lines for industrial production and demonstrated robust chain pairing with different subclasses of parent BsAbs. Thus, it can be applied to a wide variety of BsAbs both preclinically and clinically.


  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd, Yokohama, Kanagawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-factor IXa IgG fab heavy chain
A, C, E, G
227Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-factor IXa IgG fab light chain
B, D, F, H
214Homo 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: 3.19 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.937α = 90
b = 162.082β = 98.05
c = 139.014γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHENIXrefinement
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description