6O9I

Ternary complex of mouse ECD with Fab1 and Fab2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Molecular mechanism of an antagonistic antibody against glucose-dependent insulinotropic polypeptide receptor.

Min, X.Yie, J.Wang, J.Chung, B.C.Huang, C.S.Xu, H.Yang, J.Deng, L.Lin, J.Chen, Q.Abbott, C.M.Gundel, C.Thibault, S.A.Meng, T.Bates, D.L.Lloyd, D.J.Veniant, M.M.Wang, Z.

(2020) MAbs 12: 1710047-1710047

  • DOI: 10.1080/19420862.2019.1710047
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone involved in regulating glucose and lipid metabolism. GIP receptor (GIPR) antagonism is believed to offer therapeutic potential for various metabolic diseases. Pharmacological intervention of GIPR, however, has limited success due to lack of effective antagonistic reagents ...

    Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone involved in regulating glucose and lipid metabolism. GIP receptor (GIPR) antagonism is believed to offer therapeutic potential for various metabolic diseases. Pharmacological intervention of GIPR, however, has limited success due to lack of effective antagonistic reagents. Previously we reported the discovery of two mouse anti-murine GIPR monoclonal antibodies (mAbs) with distinctive properties in rodent models. Here, we report the detailed structural and biochemical characterization of these two antibodies, mAb1 and mAb2. In vitro and in vivo characterizations demonstrated mAb2 is a full GIPR antagonistic antibody and mAb1 is a non-neutralizing GIPR binder. To understand the molecular basis of these two antibodies, we determined the co-crystal structures of GIPR extracellular domain in complex with mAb1 and with mAb2 at resolutions of 2.1 and 2.6 Å, respectively. While the non-neutralizing mAb1 binds to GIPR without competing with the ligand peptide, mAb2 not only partially occludes the ligand peptide binding, but also recognizes the GIPR C-terminal stalk region in a helical conformation that acts as a molecular mimic of the ligand peptide and locks GIPR in a novel auto-inhibited state. Furthermore, administration of mAb2 in diet-induced obesity mice for 7 weeks leads to both reduction in body weight gain and improvement of metabolic profiles. In contrast, mAb1 has no effect on body weight or other metabolic improvement. Together, our studies reveal the unique molecular mechanism of action underlying the superior antagonistic activity of mAb2 and signify the promising therapeutic potential of effective GIPR antagonism for the treatment of metabolic disorders.


    Organizational Affiliation

    Departments of Therapeutics Discovery, Amgen Research, South San Francisco, CA, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab1 heavy chainA225Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab1 light chainB220Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Gastric inhibitory polypeptide receptorC137Mus musculusMutation(s): 0 
Gene Names: Gipr
Find proteins for Q0P543 (Mus musculus)
Explore Q0P543 
Go to UniProtKB:  Q0P543
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 2 heavy chainD226Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fab2 light chainE220Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, B, D, E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
DL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.43α = 87.86
b = 43.68β = 88.38
c = 133.82γ = 81.17
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-03-13 
  • Released Date: 2020-01-22 
  • Deposition Author(s): Min, X., Wang, Z.

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 2.0: 2020-02-19
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary
  • Version 2.1: 2020-02-26
    Changes: Database references
  • Version 2.2: 2020-04-01
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.3: 2020-06-10
    Changes: Database references