6C98

Crystal structure of FcRn bound to UCB-84


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.

Stoppler, D.Macpherson, A.Smith-Penzel, S.Basse, N.Lecomte, F.Deboves, H.Taylor, R.D.Norman, T.Porter, J.Waters, L.C.Westwood, M.Cossins, B.Cain, K.White, J.Griffin, R.Prosser, C.Kelm, S.Sullivan, A.H.Fox, D.Carr, M.D.Henry, A.Taylor, R.Meier, B.H.Oschkinat, H.Lawson, A.D.

(2018) PLoS Biol. 16: e2006192-e2006192

  • DOI: 10.1371/journal.pbio.2006192
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 k ...

    Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD-IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns.


    Organizational Affiliation

    Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom.,Sanofi, Strasbourg, France.,Evotec, Milton, United Kingdom.,Beryllium Discovery, Bedford, Massachusetts, United States of America.,UCB Celltech, Slough, United Kingdom.,Vertex, Milton, United Kingdom.,Midatech Pharma Plc, Milton, United Kingdom.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG receptor FcRn large subunit p51
A, C
274Homo sapiensMutation(s): 0 
Gene Names: FCGRT (FCRN)
Find proteins for P55899 (Homo sapiens)
Go to Gene View: FCGRT
Go to UniProtKB:  P55899
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ER7
Query on ER7

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Download CCD File 
B, D
1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one
C14 H11 F N4 O
VMZVIJOZARWDNG-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CYS
Query on CYS

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Download CCD File 
A, C
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ER7Kd: 80000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.270α = 90.00
b = 76.290β = 90.01
c = 138.060γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release