6DLD

Crystal structure of IgLON5/NEGR1 heterodimer

• PDB DOI: https://doi.org/10.2210/pdb6DLD/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2019-04-10 
• Deposition Author(s): Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.286 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Structure of a heterodimer of neuronal cell surface proteins

Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.

(2019) Structure 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137.95 kDa 
• Atom Count: 7,856 
• Modelled Residue Count: 1,056 
• Deposited Residue Count: 1,214 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgLON family member 5	A, C	303	Homo sapiens	Mutation(s): 0  Gene Names: IGLON5
UniProt & NIH Common Fund Data Resources
Find proteins for A6NGN9 (Homo sapiens) Explore A6NGN9  Go to UniProtKB:  A6NGN9
PHAROS:  A6NGN9 GTEx:  ENSG00000142549

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal growth regulator 1	B, D	304	Homo sapiens	Mutation(s): 0  Gene Names: NEGR1, IGLON4, UNQ2433/PRO4993
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3B1 (Homo sapiens) Explore Q7Z3B1  Go to UniProtKB:  Q7Z3B1
PHAROS:  Q7Z3B1 GTEx:  ENSG00000172260

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.286 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.341	α = 90
b = 305.799	β = 100.78
c = 60.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1450895

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary