8G80 | pdb_00008g80

Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta conformation two

PDB DOI: https://doi.org/10.2210/pdb8G80/pdb
EM Map EMD-29830: EMDB EMDataResource

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

Deposited: 2023-02-17 Released: 2025-05-14
Deposition Author(s): Boyd, R., Wang, W.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Boyd, R., Wang, W.

To be published.

Macromolecule Content

Total Structure Weight: 292.73 kDa
Atom Count: 11,067
Modelled Residue Count: 1,425
Deposited Residue Count: 2,680
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-2	A, B	870	Mus musculus	Mutation(s): 0 Gene Names: Nlgn2
UniProt
Find proteins for Q62888 (Rattus norvegicus) Go to UniProtKB: Q62888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q62888-2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q62888-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurexin-1	C, D	470	Mus musculus	Mutation(s): 0 Gene Names: Nrxn1
UniProt & NIH Common Fund Data Resources
Find proteins for E0CZA5 (Mus musculus) Explore E0CZA5 Go to UniProtKB: E0CZA5
IMPC: MGI:1096391
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E0CZA5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth C] E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	I [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]