3KJ4

Structure of rat Nogo receptor bound to 1D9 antagonist antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Resolution of disulfide heterogeneity in Nogo receptor 1 fusion proteins by molecular engineering.

Weinreb, P.H.Wen, D.Qian, F.Wildes, C.P.Garber, E.A.Walus, L.Jung, M.Y.Wang, J.Relton, J.K.Amatucci, J.Wang, R.Porreca, F.Silvian, L.Meier, W.Pepinsky, R.B.Lee, D.H.

(2010) Biotechnol Appl Biochem 57: 31-45

  • DOI: 10.1042/BA20100061

  • PubMed Abstract: 
  • NgRI (Nogo-66 receptor) is part of a signalling complex that inhibits axon regeneration in the central nervous system. Truncated soluble versions of NgRI have been used successfully to promote axon regeneration in animal models of spinal-cord injury, ...

    NgRI (Nogo-66 receptor) is part of a signalling complex that inhibits axon regeneration in the central nervous system. Truncated soluble versions of NgRI have been used successfully to promote axon regeneration in animal models of spinal-cord injury, raising interest in this protein as a potential therapeutic target. The LRR (leucine-rich repeat) regions in NgRI are flanked by N- and C-terminal disulfide-containing 'cap' domains (LRRNT and LRRCT respectively). In the present work we show that, although functionally active, the NgRI(310)-Fc fusion protein contains mislinked and heterogeneous disulfide patterns in the LRRCT domain, and we report the generation of a series of variant molecules specifically designed to prevent this heterogeneity. Using these variants we explored the effects of modifying the NgRI truncation site or the spacing between the NgRI and Fc domains, or replacing cysteines within the NgRI or IgG hinge regions. One variant, which incorporates replacements of Cys²⁶⁶ and Cys³⁰⁹ with alanine residues, completely eliminated disulfide scrambling while maintaining functional in vitro and in vivo efficacy. This modified NgRI-Fc molecule represents a significantly improved candidate for further pharmaceutical development, and may serve as a useful model for the optimization of other IgG fusion proteins made from LRR proteins.


    Organizational Affiliation

    Biogen Idec, Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. paul.weinreb@biogenidec.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab fragment 1D9 light chain
L, B
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab fragment 1D9 heavy chain
H, C
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reticulon-4 receptor
A, D
286Rattus norvegicusMutation(s): 0 
Gene Names: Rtn4r (Nogor)
Find proteins for Q99M75 (Rattus norvegicus)
Go to UniProtKB:  Q99M75
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, D
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 188.664α = 90.00
b = 125.488β = 90.00
c = 90.575γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
ADSCdata collection
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-02 
  • Released Date: 2010-09-22 
  • Deposition Author(s): Silvian, L.F.

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance