6DLF

Crystal structure of NTRI homodimer

• PDB DOI: https://doi.org/10.2210/pdb6DLF/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: 3.45 Å
• R-Value Free: 0.304 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 

Starting Model: experimental

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 68.85 kDa 
• Atom Count: 3,468 
• Modelled Residue Count: 470 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotrimin	A, B	306	Homo sapiens	Mutation(s): 0  Gene Names: NTM, IGLON2, NT, UNQ297/PRO337
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P121 (Homo sapiens) Explore Q9P121  Go to UniProtKB:  Q9P121
PHAROS:  Q9P121 GTEx:  ENSG00000182667
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q9P121-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.304 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.517	α = 90
b = 101.996	β = 90
c = 134.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	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, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary