5WHK

Crystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody.

Kenniston, J.A.Taylor, B.M.Conley, G.P.Cosic, J.Kopacz, K.J.Lindberg, A.P.Comeau, S.R.Atkins, K.Bullen, J.TenHoor, C.Adelman, B.A.Sexton, D.J.Edwards, T.E.Nixon, A.E.

(2017) J Biol Chem 292: 17449-17460

  • DOI: https://doi.org/10.1074/jbc.M117.807396
  • Primary Citation of Related Structures:  
    5WHJ, 5WHK

  • PubMed Abstract: 

    The neonatal Fc receptor FcRn plays a critical role in the trafficking of IgGs across tissue barriers and in retaining high circulating concentrations of both IgG and albumin. Although generally beneficial from an immunological perspective in maintaining IgG populations, FcRn can contribute to the pathogenesis of autoimmune disorders when an abnormal immune response targets normal biological components. We previously described a monoclonal antibody (DX-2507) that binds to FcRn with high affinity at both neutral and acidic pH, prevents the simultaneous binding of IgG, and reduces circulating IgG levels in preclinical animal models. Here, we report a 2.5 Å resolution X-ray crystal structure of an FcRn-DX-2507 Fab complex, revealing a nearly complete overlap of the IgG-Fc binding site in FcRn by complementarity-determining regions in DX-2507. This overlap explains how DX-2507 blocks IgG binding to FcRn and thereby shortens IgG half-life by preventing IgGs from recycling back into circulation. Moreover, the complex structure explains how the DX-2507 interaction is pH-insensitive unlike normal Fc interactions and how serum albumin levels are unaffected by DX-2507 binding. These structural studies could inform antibody-based therapeutic approaches for limiting the effects of IgG-mediated autoimmune disease.


  • Organizational Affiliation

    From Shire, Lexington, Massachusetts 02421, jkenniston0@shire.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DX-2507 Fab heavy chainA [auth H]219Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6BAN1 (Homo sapiens)
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Go to UniProtKB:  S6BAN1
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UniProt GroupS6BAN1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DX-2507 Fab light chainB [auth L]216Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6NS95 (Homo sapiens)
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UniProt GroupQ6NS95
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51C [auth A]297Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens)
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Go to UniProtKB:  P55899
PHAROS:  P55899
GTEx:  ENSG00000104870 
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UniProt GroupP55899
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth B]119Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.56α = 90
b = 70.45β = 90
c = 256.57γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description