› 3kj4

X-ray diffraction
3.1Å resolution

Structure of rat Nogo receptor bound to 1D9 antagonist antibody

Released:
DOI: 10.2210/pdb3kj4/pdb
PDB entry 3kj4 coloured by chain, front view.
PDB entry 3kj4 coloured by chain, side view.
PDB entry 3kj4 coloured by chain, top view.
Source organisms:
Primary publication:
Resolution of disulfide heterogeneity in Nogo receptor I fusion proteins by molecular engineering.
Weinreb PH, Wen D, Qian F, Wildes CP, Garber EA, Walus L, Jung MY, Wang J, Relton JK, Amatucci J, Wang R, Porreca F, Silvian L, Meier W, Pepinsky RB, Lee DH
Biotechnol Appl Biochem 57 31-45 (2010)
PMID: 20815818

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212705 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab fragment 1D9 light chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 219 amino acids
Theoretical weight: 24.25 KDa
Source organism: Mus musculus
Expression system: Hybridoma cells
Structure domains: Immunoglobulins
Fab fragment 1D9 heavy chain Chains: C, H
Molecule details ›
Chains: C, H
Length: 220 amino acids
Theoretical weight: 23.51 KDa
Source organism: Mus musculus
Expression system: Hybridoma cells
Structure domains: Immunoglobulins
Reticulon-4 receptor Chains: A, D
Molecule details ›
Chains: A, D
Length: 286 amino acids
Theoretical weight: 31.8 KDa
Source organism: Rattus norvegicus
Expression system: CHO
UniProt:
  • Canonical: Q99M75 (Residues: 27-312; Coverage: 64%)
Gene names: Nogor, Rtn4r
Sequence domains: Leucine rich repeat
Structure domains: Ribonuclease Inhibitor

Ligands and Environments

4 bound ligands:
Ligand MAN 1 x MAN
Ligand ZN 2 x ZN
Ligand NDG 4 x NDG
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 188.664Å b: 125.488Å c: 90.575Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.253 0.318
Expression system: CHO

Quick links

Citations

1 review citation

How does Nogo receptor influence demyelination and remyelination in the context of multiple sclerosis?
Rashidbenam et al. (2023)
6 other articles

2 mentions without citation

A complete, multi-level conformational clustering of antibody complementarity-determining regions.
Nikoloudis et al. (2014)
1 more