8G7Y: Neuroligin-2

Cryo-EM Structure of full length Neuroligin-2 from mouse with Neurexin-1 beta. Determined by electron microscopy at 3.92 Å resolution. Released 14 May 2025.

Method
Electron microscopy
Resolution
3.92 Å
Organism
Mus musculus
Chains
3
Atoms
9,783
Mol. weight
241.02 kDa
Ligands
CA, NAG
Released
14 May 2025

Explore 8G7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G7Y contains 61 α-helices and 59 β-strands across 3 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: 29 helices, 20 β-strands

ElementResiduesLengthSheet
β-strand43-4641
β-strand49-5241
β-strand66-6942
β-strand7013
β-strand71-7332
α-helix89-935
β-strand96-9831
β-strand10013
α-helix102-1065
α-helix121-1255
α-helix127-1337
β-strand143-14972
β-strand177-18372
α-helix193-1953
α-helix199-2057
β-strand208-21252
α-helix217-2204
β-strand223-22644
β-strand229-23024
α-helix233-24614
α-helix249-2524
β-strand254-263102
α-helix266-27611
β-strand286-28832
β-strand30115
α-helix304-31512
α-helix322-3309
α-helix334-3396
α-helix344-3452
β-strand35415
α-helix364-3707
β-strand377-38372
α-helix388-3903
α-helix393-3964
α-helix403-41715
α-helix425-43410
α-helix438-4403
α-helix445-45612
α-helix457-4615
α-helix462-47312
β-strand478-48362
α-helix504-5085
α-helix510-5134
α-helix525-54319
β-strand580-58342
β-strand588-59032
α-helix595-5995
α-helix600-6045
α-helix605-6073
Chain B: 29 helices, 21 β-strands
ElementResiduesLengthSheet
β-strand43-4646
β-strand49-5246
β-strand54-5637
β-strand66-6837
β-strand7018
β-strand72-7329
α-helix89-924
β-strand96-9726
β-strand10018
α-helix102-1076
α-helix116-1183
α-helix121-1255
α-helix127-1337
β-strand143-14539
β-strand14817
β-strand177-183710
α-helix193-1953
α-helix200-2056
β-strand208-210310
β-strand211-21229
α-helix218-2214
β-strand223111
β-strand230111
α-helix233-24816
α-helix249-2524
β-strand254-2641110
α-helix266-27611
β-strand286-290510
α-helix304-31512
α-helix322-3309
α-helix334-3385
α-helix344-3452
α-helix364-3707
β-strand378-383610
α-helix394-3963
α-helix403-41715
α-helix425-43410
α-helix438-4403
α-helix445-45612
α-helix457-4615
α-helix462-47312
β-strand478-483610
α-helix503-5075
α-helix510-5134
α-helix525-54420
β-strand580-583410
β-strand589-590210
α-helix595-5995
α-helix600-6045
α-helix605-6073
Chain C: 3 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand86-88312
β-strand94-99613
α-helix102-1043
β-strand110-118912
β-strand124-130714
β-strand131115
β-strand138-144714
β-strand147-153714
β-strand159-162414
β-strand174-181812
β-strand184-189612
α-helix193-1942
β-strand195-197312
β-strand240115
β-strand242-243213
β-strand244-245214
β-strand257-263712
β-strand266112
α-helix268-2736
β-strand279-283513
β-strand286-287212

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Neuroligin-2A, Bprotein870Mus musculusQ69ZK9 (AlphaFold model)
Neurexin-1Cprotein461Mus musculusE0CZA5 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>8G7Y_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), FASTA
>8G7Y_2 Neurexin-1 (chains C)
MYQRMLRCGADLGSPGGGSGGGAGGRLALIWIVPLTLGGLLGVAWGASSLGAHHIHHFHG
SSKEFEQKLISEEDLGFEIDKVWHDFPATSPIAIYRSPASLRGGHAGTTYIFSKGGGQIT
YKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTD
DIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGG
KEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPSSMTTESTATAMQSE
MSTSIMETTTTLATSTARRGKPPTKEPISQTTDDILVASAECPSDDEDIDPCEPSSGGLA
NPTRVGGREPYPGSAEVIRESSSTTGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVD
ESRNYISNSAQSNGAVVKEKQPSSAKSANKNKKNKDKEYYV

Ligands and cofactors

IDNameFormulaCopies
CACalcium ionCa1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O65

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:

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