3B3Q: Synaptic adhesion complex

Crystal structure of a synaptic adhesion complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Jan 2008.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 12,952
Mol. weight: 173.74 kDa
Ligands: NAG, CA
Released: 15 Jan 2008

Explore 3B3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B3Q contains 64 α-helices and 70 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: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	1
β-strand	60-63	4	1
β-strand	65-67	3	2
β-strand	77-84	8	2
α-helix	91-93	3
α-helix	100-103	4
β-strand	107-109	3	1
β-strand	111	1	2
α-helix	113-115	3
β-strand	116	1	3
α-helix	117-118	2
α-helix	133-137	5
α-helix	139-145	7
β-strand	149	1	3
β-strand	155-160	6	2
α-helix	192	1
β-strand	193-198	6	2
α-helix	209-211	3
α-helix	215-221	7
β-strand	224-228	5	2
α-helix	233-237	5
α-helix	249-264	16
α-helix	266-268	3
β-strand	270-280	11	2
α-helix	282-290	9
β-strand	311-315	5	2
β-strand	326	1	4
α-helix	329-339	11
α-helix	347-356	10
α-helix	359-363	5
β-strand	379	1	4
α-helix	389-395	7
β-strand	402-408	7	2
α-helix	413-416	4
α-helix	417-419	3
α-helix	428-443	16
α-helix	451-459	9
α-helix	469-481	13
α-helix	482-486	5
α-helix	487-498	12
β-strand	503-508	6	2
α-helix	529-532	4
α-helix	550-569	20
α-helix	596-598	3
β-strand	604-608	5	2
β-strand	613-616	4	2
α-helix	620-624	5
α-helix	625-629	5
α-helix	630-633	4

Chain B: 30 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	5
β-strand	60-63	4	5
β-strand	65-67	3	6
β-strand	77-80	4	6
β-strand	81	1	7
β-strand	82-84	3	6
α-helix	91-93	3
α-helix	100-103	4
β-strand	107-109	3	5
β-strand	111	1	7
α-helix	113-115	3
β-strand	116	1	8
α-helix	117-118	2
α-helix	133-136	4
α-helix	139-145	7
β-strand	149	1	8
β-strand	155-160	6	6
α-helix	192	1
β-strand	193-198	6	6
α-helix	209-211	3
α-helix	215-221	7
β-strand	224-228	5	6
α-helix	233-237	5
α-helix	249-264	16
α-helix	266-268	3
β-strand	270-280	11	6
α-helix	282-290	9
β-strand	311-315	5	6
β-strand	326	1	9
α-helix	329-339	11
α-helix	347-356	10
α-helix	359-363	5
β-strand	379	1	9
α-helix	389-395	7
β-strand	402-408	7	6
α-helix	413-416	4
α-helix	417-419	3
α-helix	428-443	16
α-helix	451-459	9
α-helix	469-481	13
α-helix	482-486	5
α-helix	487-498	12
β-strand	503-508	6	6
α-helix	529-532	4
α-helix	550-569	20
α-helix	596-598	3
β-strand	604-608	5	6
β-strand	613-616	4	6
α-helix	620-624	5
α-helix	625-629	5
α-helix	630-633	4

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	87-99	13	10
β-strand	108	1	11
β-strand	110-119	10	10
β-strand	123-131	9	10
β-strand	138-144	7	10
β-strand	147-153	7	10
β-strand	159-162	4	10
β-strand	174-181	8	10
β-strand	184-188	5	10
α-helix	193-194	2
β-strand	195-197	3	10
β-strand	237	1	11
β-strand	240-245	6	10
β-strand	256-263	8	10
β-strand	266-267	2	10
α-helix	268-272	5
β-strand	279-286	8	10

Chain F: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	86-99	14	12
β-strand	108	1	13
β-strand	110-119	10	12
β-strand	123-131	9	12
β-strand	138-144	7	12
β-strand	147-153	7	12
β-strand	159-162	4	12
β-strand	174-181	8	12
β-strand	184-188	5	12
α-helix	193-194	2
β-strand	195-197	3	12
β-strand	237	1	13
β-strand	240-245	6	12
β-strand	256-263	8	12
β-strand	266-267	2	12
α-helix	268-272	5
β-strand	279-288	10	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nlgn1 protein	A, B	protein	577	Mus musculus	Q99K10 (AlphaFold model)
NRXN1 protein	E, F	protein	197	Homo sapiens	P58400 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3B3Q_1 Nlgn1 protein (chains A, B)
ADPHHHHHHENLYFQGQKLDDVDPLVTTNFGKIRGIKKELNNEILGPVIQFLGVPYAAPP
TGEHRFQPPEPPSPWSDIRNATQFAPVCPQNIIDGRLPEVMLPVWFTNNLDVVSSYVQDQ
SEDCLYLNIYVPTEDDIRDSGGPKPVMVYIHGGSYMEGTGNLYDGSVLASYGNVIVITVN
YRLGVLGFLSTGDQAAKGNYGLLDLIQALRWTSENIGFFGGDPLRITVFGSGAGGSCVNL
LTLSHYSEGLFQRAIAQSGTALSSWAVSFQPAKYARILATKVGCQVSDTVELVECLQKKP
YKELVDQDVQPARYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVEN
IVDSDDGVSASDFDFAVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRHNPETRRKTLLA
LFTDHQWVAPAVATADLHSNFGSPTYFYAFYHHCQTDQVPAWADAAHGDEVPYVLGIPMI
GPTELFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWTRY
SQKDQLYLHIGLKPRVKEHYRANKVNLWLELVPHLHN

Sequence of entity 2 (E, F), FASTA

>3B3Q_2 NRXN1 protein (chains E, F)
HSAFAADPGHAGTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSS
SGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSW
PVIERYPAGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIV
GNVRLVGEVPHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CA	Calcium ion	Ca	2

Primary citation

Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions. Chen, X., Liu, H., Shim, A.H. et al. Nat Struct Mol Biol (2008) 15:50-56. DOI 10.1038/nsmb1350 · PubMed

Other PDB entries of the same protein (UniProt Q99K10 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G7D 3.28 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse

Browse structure collections

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