Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33218.83 
• Atom Count: 2320 
• Residue Count: 285 
• Unique protein chains: 1

1OZN

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

• DOI: 10.2210/pdb1OZN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni


• Deposited: 2003-04-09 Released: 2003-05-20 
• Deposition Author(s): He, X., Bazan, J.F., Park, J.B., McDermott, G., He, Z., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.198 
• R-Value Work: 0.167 

Literature

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

• PubMed: 12718853 


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Reticulon 4 receptor	A	285	Homo sapiens	Mutation(s): 0  Gene Names: RTN4R (NOGOR)
Find proteins for Q9BZR6 (Homo sapiens) Go to Gene View: RTN4R Go to UniProtKB:  Q9BZR6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NDG	A	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACY	A	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.198 
• R-Value Work: 0.167 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 32.206	α = 85.02
b = 33.915	β = 75.91
c = 60.221	γ = 67.96

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
CNS	refinement
SOLVE	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-09 
• Released Date: 2003-05-20 
• Deposition Author(s): He, X., Bazan, J.F., Park, J.B., McDermott, G., He, Z., Garcia, K.C.

Revision History 

• Version 1.0: 2003-05-20
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance