3M17

Crystal structure of human FcRn with a monomeric peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray crystal structures of monomeric and dimeric peptide inhibitors in complex with the human neonatal Fc receptor, FcRn.

Mezo, A.R.Sridhar, V.Badger, J.Sakorafas, P.Nienaber, V.

(2010) J Biol Chem 285: 27694-27701

  • DOI: 10.1074/jbc.M110.120667
  • Primary Citation of Related Structures:  
    3M17, 3M1B

  • PubMed Abstract: 
  • The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A ...

    The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 A resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.


    Organizational Affiliation

    Biogen Idec, Syntonix Subsidiary, Waltham, Massachusetts 02451, USA. adam.mezo@biogenidec.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51A, C, E, G267Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
PHAROS:  P55899
Entity Groups  
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UniProt GroupP55899
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, D, F, H99Homo 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
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
monomeric peptide inhibitorI, J, K, L15N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
LE1
Query on LE1
I, J, K, L L-PEPTIDE LINKINGC5 H11 N O2 SVAL
MLE
Query on MLE
I, J, K, L L-PEPTIDE LINKINGC7 H15 N O2LEU
SAR
Query on SAR
I, J, K, L PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001091
Query on PRD_001091
I, J, K, Lmonomeric peptide inhibitorPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.264 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.32α = 90
b = 118.3β = 90
c = 248.33γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Derived calculations
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2022-05-04
    Changes: Database references, Derived calculations, Structure summary