8G80: Full length Neuroligin-2 from Mouse

Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta conformation two. Determined by electron microscopy at 3.25 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Mus musculus
Chains: 4
Atoms: 11,067
Mol. weight: 292.73 kDa
Ligands: NAG, CA
Released: 14 May 2025

Explore 8G80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G80 contains 52 α-helices and 62 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	1
β-strand	50-52	3	1
β-strand	54	1	2
α-helix	56-58	3
β-strand	66-73	8	2
β-strand	96-98	3	1
α-helix	102-107	6
α-helix	121-125	5
α-helix	127-133	7
β-strand	143-149	7	2
β-strand	179-182	4	2
α-helix	200-205	6
β-strand	208-213	6	2
α-helix	218-221	4
α-helix	233-248	16
α-helix	250-252	3
β-strand	259-264	6	2
α-helix	266-275	10
β-strand	286-290	5	2
β-strand	301	1	3
α-helix	304-315	12
α-helix	322-329	8
α-helix	334-338	5
β-strand	354	1	3
α-helix	364-367	4
β-strand	377-383	7	2
α-helix	387-389	3
α-helix	403-417	15
α-helix	421-423	3
α-helix	426-434	9
α-helix	445-456	12
α-helix	457-461	5
α-helix	462-473	12
β-strand	478-483	6	2
α-helix	504-507	4
α-helix	525-544	20
β-strand	580-581	2	2
β-strand	589-590	2	2
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-607	3

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	4
β-strand	50-52	3	4
β-strand	54	1	5
β-strand	66-73	8	5
β-strand	96-98	3	4
α-helix	102-106	5
α-helix	121-125	5
α-helix	127-133	7
β-strand	143-149	7	5
β-strand	177-182	6	5
α-helix	199-205	7
β-strand	208-212	5	5
α-helix	218-221	4
α-helix	233-248	16
β-strand	254-264	11	5
α-helix	266-273	8
β-strand	286-290	5	5
β-strand	301	1	6
α-helix	304-315	12
α-helix	322-329	8
α-helix	343-345	3
β-strand	354	1	6
α-helix	364-369	6
β-strand	377-383	7	5
α-helix	403-417	15
α-helix	427-434	8
α-helix	438-440	3
α-helix	448-456	9
α-helix	457-461	5
α-helix	462-472	11
β-strand	478-483	6	5
α-helix	504-507	4
α-helix	525-544	20
β-strand	580-581	2	5
β-strand	589-590	2	5
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-607	3

Chain C: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	86-99	14	7
β-strand	108	1	8
β-strand	110-119	10	7
β-strand	124-131	8	7
β-strand	138-144	7	7
β-strand	147-153	7	7
β-strand	158-162	5	7
β-strand	174-181	8	7
β-strand	184-189	6	7
α-helix	193-194	2
β-strand	195-197	3	7
β-strand	237	1	8
β-strand	240-245	6	7
β-strand	256-263	8	7
β-strand	266-267	2	7
α-helix	268-273	6
β-strand	280-288	9	7

Chain D: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	87-99	13	9
α-helix	102-104	3
β-strand	108	1	10
β-strand	110-118	9	9
β-strand	123-131	9	9
β-strand	138-144	7	9
β-strand	147-153	7	9
β-strand	158-162	5	9
β-strand	174-181	8	9
β-strand	184-189	6	9
α-helix	193-194	2
β-strand	195-197	3	9
β-strand	237	1	10
β-strand	240-245	6	9
β-strand	257-263	7	9
β-strand	266-267	2	9
α-helix	268-272	5
β-strand	279-287	9	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuroligin-2	A, B	protein	870	Mus musculus	Q69ZK9 (AlphaFold model)
Neurexin-1	C, D	protein	470	Mus musculus	E0CZA5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8G80_1 Neuroligin-2 (chains A, B)
MALPRCMWPNYVWRAMMACVVHRGSGAPLTLCLLGCLLQTFHVLSQKYPYDVPDYAQRGG
GGPGGGAPGGPGLGLGSLGEERFPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPP
LGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQS
EDCLYLNLYVPTEDDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYR
LGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLI
LSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSR
ELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSA
ESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALF
TDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGA
TDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNS
KEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHNLHTELFTTTTRLPPYATRWPPRTPG
PGTSGTRRPPPPATLPPESDIDLGPRAYDRFPGDSRDYSTELSVTVAVGASLLFLNILAF
AALYYKRDRRQELRCRRLSPPGGSGSGVPGGGPLLPTAGRELPPEEELVSLQLKRGGGVG
ADPAEALRPACPPDYTLALRRAPDDVPLLAPGALTLLPSGLGPPPPPPPPSLHPFGPFPP
PPPTATSHNNTLPHPHSTTRVSNSLEVLFQ

Sequence of entity 2 (C, D), FASTA

>8G80_2 Neurexin-1 (chains C, D)
MYQRMLRCGADLGSPGGGSGGGAGGRLALIWIVPLTLGGLLGVAWGASSLGAHHIHHFHG
SSKEFEQKLISEEDLGFEIDKVWHDFPATSPIAIYRSPASLRGGHAGTTYIFSKGGGQIT
YKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTD
DIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGG
KEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPSSMTTESTATAMQSE
MSTSIMETTTTLATSTARRGKPPTKEPISQTTDDILVASAECPSDDEDIDPCEPSSGGLA
NPTRVGGREPYPGSAEVIRESSSTTGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVD
ESRNYISNSAQSNGAVVKEKQPSSAKSANKNKKNKDKEYYVSNSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
CA	Calcium ion	Ca	2

Primary citation

Weaker neuroligin 2-neurexin beta 1 interaction tethers membranes and recruits gephyrin at membrane junctions through clustering. Boyd, R., Jaqaman, K., Wang, W. Sci Adv (2026) 12:eads9732-eads9732. DOI 10.1126/sciadv.ads9732 · PubMed

Other PDB entries of the same protein (UniProt Q69ZK9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G7Z 3.22 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta…
8G81 3.22 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta…
8G7D 3.28 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse
3BL8 3.3 Å, Crystal structure of the extracellular domain of neuroligin 2A from mouse
8G7Y 3.92 Å, Cryo-EM Structure of full length Neuroligin-2 from mouse with Neurexin-1 beta

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