6U7N

Crystal structure of neurotrimin (NTM)

• PDB DOI: https://doi.org/10.2210/pdb6U7N/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2019-09-03 Released: 2020-08-12 
• Deposition Author(s): Machius, M., Venkannagari, H., Misra, A., Rudenko, G., Rush, S.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.250 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

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: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 36.24 kDa 
• Atom Count: 2,100 
• Modelled Residue Count: 256 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotrimin	A	314	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.250 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.049	α = 90
b = 106.049	β = 90
c = 227.819	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Machius, M., Venkannagari, H., Misra, A., Rudenko, G., Rush, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01MH077303

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description