3KJ4

Structure of rat Nogo receptor bound to 1D9 antagonist antibody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    3KJ4

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment 1D9 light chainB, L219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment 1D9 heavy chainC, H220Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reticulon-4 receptorA, D286Rattus norvegicusMutation(s): 0 
Gene Names: Nogo Receptor, Nogor, Rtn4r
Find proteins for Q99M75 (Rattus norvegicus)
Explore Q99M75 
Go to UniProtKB:  Q99M75
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.664α = 90
b = 125.488β = 90
c = 90.575γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary