8G7D | pdb_00008g7d

Cryo-EM structure of full length Neuroligin-2 from Mouse

• PDB DOI: https://doi.org/10.2210/pdb8G7D/pdb
• EM Map EMD-29811: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-02-16 Released: 2025-05-14 
• Deposition Author(s): Boyd, R., Wang, W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), McKnight Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of full length mouse Neuroligin-2 at 3.28 Angstroms resolution

Boyd, R., Wang, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 191.34 kDa 
• Atom Count: 8,346 
• Modeled Residue Count: 1,076 
• Deposited Residue Count: 1,740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-1,Neuroligin-2	A, B	870	Mus musculus	Mutation(s): 0  Gene Names: Nlgn1, Kiaa1070, Nlgn2, Kiaa1366
UniProt
Find proteins for Q69ZK9 (Mus musculus) Explore Q69ZK9  Go to UniProtKB:  Q69ZK9
Find proteins for Q99K10 (Mus musculus) Explore Q99K10  Go to UniProtKB:  Q99K10
UniProt Groups	Q99K10Q69ZK9
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q69ZK9-1Q99K10-1

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: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3
MODEL REFINEMENT	PHENIX	1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Boyd, R., Wang, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1R25Gm146860
McKnight Foundation	United States	2022 Scholar Award

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release