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 1.1 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: 10.1074/jbc.M117.807396
  • Primary Citation of Related Structures:  
    5WHK, 5WHJ

  • 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 ...

    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: 

    Dyax Corp., Burlington, Massachusetts 01803.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DX-2507 Fab heavy chainH219Homo sapiensMutation(s): 0 
Find proteins for S6BAN1 (Homo sapiens)
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Go to UniProtKB:  S6BAN1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DX-2507 Fab light chainL216Homo sapiensMutation(s): 0 
Gene Names: IGL@
Find proteins for Q6NS95 (Homo sapiens)
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Go to UniProtKB:  Q6NS95
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51A297Homo sapiensMutation(s): 0 
Gene Names: FCGRT, FCRN
Find proteins for P55899 (Homo sapiens)
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Go to UniProtKB:  P55899
NIH Common Fund Data Resources
PHAROS  P55899
GTEx  ENSG00000104870
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB119Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE
Download Ideal Coordinates CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A, H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
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 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references