7CEG: Complex between mouse PTP delta and neuroligin-3

Crystal structure of the complex between mouse PTP delta and neuroligin-3. Determined by X-ray diffraction at 3.85 Å resolution. Released 24 Feb 2021.

Method: X-ray diffraction
Resolution: 3.85 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,273
Mol. weight: 107.78 kDa
Ligands: NAG
Released: 24 Feb 2021

Explore 7CEG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CEG contains 38 α-helices and 56 β-strands across 2 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: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	1
β-strand	40-43	4	2
β-strand	48-57	10	1
β-strand	61-66	6	3
β-strand	77-80	4	1
β-strand	86-91	6	1
β-strand	102-108	7	3
β-strand	113-119	7	3
β-strand	120-123	4	2
β-strand	134-137	4	4
β-strand	142-143	2	2
α-helix	149	1
β-strand	150-152	3	5
β-strand	155-157	3	4
α-helix	161-162	2
β-strand	163-168	6	2
β-strand	171-172	2	2
β-strand	182-186	5	5
β-strand	191-195	5	5
α-helix	200-202	3
β-strand	204-211	8	2
β-strand	216-218	3	2
β-strand	222-225	4	2
β-strand	231-237	7	6
β-strand	250-252	3	7
β-strand	255-259	5	6
α-helix	261-262	2
β-strand	263-267	5	8
β-strand	272	1	8
β-strand	281	1	8
β-strand	283	1	6
β-strand	286-288	3	7
β-strand	295-302	8	8
β-strand	307-314	8	8
α-helix	316-326	11
β-strand	327-331	5	9
β-strand	335-339	5	9
β-strand	350-357	8	10
α-helix	363-364	2
β-strand	365-370	6	10
β-strand	374-378	5	9
α-helix	380-381	2
β-strand	386-393	8	10
β-strand	398-401	4	10
β-strand	405-406	2	10

Chain B: 31 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	40-43	4	11
β-strand	46-49	4	11
β-strand	51-53	3	12
α-helix	61-62	2
β-strand	63-70	8	12
α-helix	86-89	4
β-strand	93-95	3	11
α-helix	99-101	3
β-strand	102	1	13
α-helix	103	1
α-helix	118-122	5
α-helix	124-131	8
β-strand	134	1	13
β-strand	140-146	7	12
α-helix	176	1
β-strand	177-185	9	12
α-helix	193-195	3
α-helix	199-205	7
β-strand	208-212	5	12
α-helix	218-221	4
β-strand	226	1	14
β-strand	229	1	14
α-helix	233-248	16
α-helix	250-252	3
β-strand	254-265	12	12
α-helix	266-276	11
β-strand	286-290	5	12
α-helix	304-315	12
α-helix	322-331	10
α-helix	334-339	6
α-helix	364-370	7
β-strand	377-383	7	12
α-helix	388-392	5
α-helix	403-418	16
α-helix	425-434	10
α-helix	444-456	13
α-helix	457-461	5
α-helix	462-472	11
β-strand	478-483	6	12
α-helix	504-508	5
α-helix	510-512	3
α-helix	525-544	20
α-helix	571-573	3
β-strand	579-583	5	12
β-strand	588-591	4	12
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-609	5
α-helix	612-614	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform C of Receptor-type tyrosine-protein phosphatase delta	A	protein	386	Mus musculus	Q64487 (AlphaFold model)
Neuroligin-3	B	protein	579	Mus musculus	Q8BYM5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7CEG_1 Isoform C of Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGALQIEQSEESDQGKYE
CVATNSAGTRYSAPANLYVRVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKWM
LGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVKALPKPPGTPV
VTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSVAGLSPYSDYE
FRVVAVNNIGRGPASEPVLTQKHHHH

Sequence of entity 2 (B), FASTA

>7CEG_2 Neuroligin-3 (chains B)
PAPTVNTHFGKLRGARVPLPSEILGPVDQYLGVPYAAPPIGEKRFLPPEPPPSWSGIRNA
THFPPVCPQNIHTAVPEVMLPVWFTANLDIVATYIQEPNEDCLYLNVYVPTEDGSGAKKQ
GEDLADNDGDEDEDIRDSGAKPVMVYIHGGSYMEGTGNMIDGSVLASYGNVIVITLNYRV
GVLGFLSTGDQAAKGNYGLLDQIQALRWVSENIAFFGGDPRRITVFGSGIGASCVSLLTL
SHHSEGLFQRAIIQSGSALSSWAVNYQPVKYTSLLADKVGCNVLDTVDMVDCLRQKSAKE
LVEQDIQPARYHVAFGPVIDGDVIPDDPEILMEQGEFLNYDIMLGVNQGEGLKFVEGVVD
PEDGVSGTDFDYSVSNFVDNLYGYPEGKDTLRETIKFMYTDWADRDNPETRRKTLVALFT
DHQWVEPSVVTADLHARYGSPTYFYAFYHHCQSLMKPAWSDAAHGDEVPYVFGVPMVGPT
DLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNKPVPQDTKFIHTKANRFEEVAWSKYNPR
DQLYLHIGLKPRVRDHYRATKVAFWKHLVPHLYNLHDMF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice. Yoshida, T., Yamagata, A., Imai, A. et al. Nat Commun (2021) 12:1848-1848. DOI 10.1038/s41467-021-22059-6 · PubMed

Other PDB entries of the same protein (UniProt Q64487 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KIP 1.91 Å, Crystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM…
4YFE 1.97 Å, Crystal structure of PTP delta Fn1-Fn2
5Y32 2.7 Å, Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1
5XWU 3.16 Å, Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig
4YFD 3.25 Å, Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
4Y61 3.36 Å, Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1
4YFG 3.49 Å, Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1
5XWT 4.18 Å, Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig
4YH7 4.4 Å, Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Browse structure collections

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