5UBX

Crystal structure of a mutant mIgG2b Fc heterodimer in complex with Protein A peptide analog Z34C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Modulation of protein A binding allows single-step purification of mouse bispecific antibodies that retain FcRn binding.

Zwolak, A.Armstrong, A.A.Tam, S.H.Pardinas, J.R.Goulet, D.R.Zheng, S.Brosnan, K.Emmell, E.Luo, J.Gilliland, G.L.Chiu, M.L.

(2017) MAbs 9: 1306-1316

  • DOI: https://doi.org/10.1080/19420862.2017.1375639
  • Primary Citation of Related Structures:  
    5UBX

  • PubMed Abstract: 

    The increased number of bispecific antibodies (BsAb) under therapeutic development has resulted in a need for mouse surrogate BsAbs. Here, we describe a one-step method for generating highly pure mouse BsAbs suitable for in vitro and in vivo studies. We identify two mutations in the mouse IgG2a and IgG2b Fc region: one that eliminates protein A binding and one that enhances protein A binding by 8-fold. We show that BsAbs harboring these mutations can be purified from the residual parental monoclonal antibodies in one step using protein A affinity chromatography. The structural basis for the effects of these mutations was analyzed by X-ray crystallography. While the mutation that disrupted protein A binding also inhibited FcRn interaction, a bispecific mutant in which one subunit retained the ability to bind protein A could still interact with FcRn. Pharmacokinetic analysis of the serum half-lives of the mutants showed that the mutant BsAb had a serum half-life comparable to a wild-type Ab. The results describe a rapid method for generating panels of mouse BsAbs that could be used in mouse studies.


  • Organizational Affiliation

    a Biologics Discovery , Janssen Research & Development, LLC , Spring House , PA , USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ig gamma-2B chain C region230Mus musculusMutation(s): 4 
Gene Names: Igh-3
UniProt
Find proteins for P01867 (Mus musculus)
Explore P01867 
Go to UniProtKB:  P01867
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01867
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ig gamma-2B chain C region236Mus musculusMutation(s): 2 
Gene Names: Igh-3
UniProt
Find proteins for P01867 (Mus musculus)
Explore P01867 
Go to UniProtKB:  P01867
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01867
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide analog of B-domain from Protein A - Z34CC [auth Z]34Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]6N/A
Glycosylation Resources
GlyTouCan:  G55061AW
GlyCosmos:  G55061AW
GlyGen:  G55061AW
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-glucopyranoseE [auth D]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80858MF
GlyCosmos:  G80858MF
GlyGen:  G80858MF
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.49α = 90
b = 101.49β = 90
c = 135.07γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary