7CEE

Crystal structure of mouse neuroligin-3

• PDB DOI: https://doi.org/10.2210/pdb7CEE/pdb

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


• Deposited: 2020-06-23 Released: 2021-02-24 
• Deposition Author(s): Yamagata, A., Yoshida, T., Shiroshima, T., Maeda, A., Fukai, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

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: gel filtration

Macromolecule Content

• Total Structure Weight: 146.87 kDa 
• Atom Count: 8,489 
• Modelled Residue Count: 1,067 
• Deposited Residue Count: 1,310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-3	A, B	655	Mus musculus	Mutation(s): 0  Gene Names: Nlgn3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BYM5 (Mus musculus) Explore Q8BYM5  Go to UniProtKB:  Q8BYM5
IMPC:  MGI:2444609

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [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: 2.76 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.842	α = 90
b = 167.142	β = 90
c = 177.95	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Yamagata, A., Yoshida, T., Shiroshima, T., Maeda, A., Fukai, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04749
Japan Society for the Promotion of Science (JSPS)	Japan	JP25293057
Japan Society for the Promotion of Science (JSPS)	Japan	JP24247014
Japan Science and Technology	Japan	JPMJCR12M5

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description