3M1B

Crystal structure of human FcRn with a dimeric peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.397 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.318 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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 pre ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG receptor FcRn large subunit p51A, C, E, G267Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
NIH Common Fund Data Resources
PHAROS  P55899
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulinB, D, F, H99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DIMERIC PEPTIDE INHIBITORI, J16N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000816
Query on PRD_000816
I, JDIMERIC PEPTIDE INHIBITORP /  Inhibitor

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Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
LE1
Query on LE1
I,JL-PEPTIDE LINKINGC5 H11 N O2 SVAL
MLE
Query on MLE
I,JL-PEPTIDE LINKINGC7 H15 N O2LEU
SAR
Query on SAR
I,JPEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.397 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.318 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.05α = 90
b = 158.431β = 90.11
c = 82.539γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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