1.5A Crystal Structure of the Nogo Receptor Ligand Binding Domain Reveals a Convergent Recognition Scaffold Mediating Inhibition of Myelination

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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This is version 2.0 of the entry. See complete history


Structure of the Nogo Receptor Ectodomain. A Recognition module implicated in Myelin Inhibition.

He, X.L.Bazan, J.F.McDermott, G.Park, J.B.Wang, K.Tessier-Lavigne, M.He, Z.Garcia, K.C.

(2003) Neuron 38: 177-185

  • DOI: https://doi.org/10.1016/s0896-6273(03)00232-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Failure of axon regeneration in the adult mammalian central nervous system (CNS) is at least partly due to inhibitory molecules associated with myelin. Recent studies suggest that an axon surface protein, the Nogo receptor (NgR), may play a role in this process through an unprecedented degree of crossreactivity with myelin-associated inhibitory ligands. Here, we report the 1.5 A crystal structure and functional characterization of a soluble extracellular domain of the human Nogo receptor. Nogo receptor adopts a leucine-rich repeat (LRR) module whose concave exterior surface contains a broad region of evolutionarily conserved patches of aromatic residues, possibly suggestive of degenerate ligand binding sites. A deep cleft at the C-terminal base of the LRR may play a role in NgR association with the p75 coreceptor. These results now provide a detailed framework for focused structure-function studies aimed at assessing the physiological relevance of NgR-mediated protein-protein interactions to axon regeneration inhibition.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reticulon 4 receptor285Homo sapiensMutation(s): 0 
Gene Names: RTN4R OR NOGOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZR6 (Homo sapiens)
Explore Q9BZR6 
Go to UniProtKB:  Q9BZR6
GTEx:  ENSG00000040608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZR6
Glycosylation Sites: 2Go to GlyGen: Q9BZR6-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G46299JT
GlyCosmos:  G46299JT
GlyGen:  G46299JT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G35926TG
GlyCosmos:  G35926TG
GlyGen:  G35926TG
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.206α = 85.02
b = 33.915β = 75.91
c = 60.221γ = 67.96
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary