5FTT: Netrin receptor UNC5D

Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR). Determined by X-ray diffraction at 3.4 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: RATTUS NORVEGICUS, MUS MUSCULUS
Chains: 8
Atoms: 19,610
Mol. weight: 318.36 kDa
Ligands: CA, NAG
Released: 4 May 2016

Explore 5FTT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FTT contains 58 α-helices and 231 β-strands across 8 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: 13 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	47-49	3
β-strand	50	1	1
β-strand	53-54	2	2
α-helix	57-61	5
β-strand	62-63	2	3
β-strand	64	1	4
β-strand	67	1	4
β-strand	71	1	5
β-strand	74-76	3	2
β-strand	80-85	6	6
β-strand	88-89	2	6
α-helix	90-91	2
α-helix	92-94	3
β-strand	96-98	3	2
α-helix	108-109	2
β-strand	110-113	4	2
β-strand	114	1	5
α-helix	118-122	5
β-strand	131-137	7	6
β-strand	142-144	3	6
β-strand	148-149	2	6
β-strand	151-152	2	3
β-strand	154-155	2	7
β-strand	161	1	8
α-helix	162-165	4
β-strand	167-168	2	9
β-strand	174-177	4	10
β-strand	179	1	8
α-helix	180-182	3
β-strand	183-184	2	7
β-strand	188-193	6	11
β-strand	197	1	11
β-strand	206-208	3	10
β-strand	213-216	4	10
β-strand	225-232	8	11
β-strand	237-239	3	11
α-helix	241-242	2
β-strand	243-245	3	11
β-strand	246-247	2	9
β-strand	249	1	12
α-helix	253-256	4
α-helix	258-261	4
β-strand	267-274	8	13
α-helix	281-282	2
β-strand	283	1	12
α-helix	286-290	5
β-strand	294-301	8	13

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	41-43	3	14
β-strand	46-48	3	14
β-strand	67-69	3	14
α-helix	83-86	4
β-strand	92-94	3	14
β-strand	102	1	15
β-strand	113-115	3	14
β-strand	123	1	15
β-strand	124	1	16
α-helix	126-131	6
β-strand	137-139	3	14
β-strand	150	1	16
α-helix	155-157	3
β-strand	163-165	3	14
β-strand	184-186	3	14
β-strand	195	1	17
α-helix	197-200	4
β-strand	208-210	3	14
β-strand	221	1	17
α-helix	226-228	3
β-strand	234-236	3	14
α-helix	245-246	2
β-strand	256-258	3	14
α-helix	269-271	3
β-strand	280-282	3	14
β-strand	304-306	3	14
β-strand	312-313	2	18
α-helix	319-326	8
β-strand	333-335	3	14
β-strand	338	1	19
β-strand	339-341	3	18
β-strand	349	1	19

Chain C: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	101-104	4	20
β-strand	108-112	5	21
α-helix	117	1
β-strand	118-127	10	20
β-strand	128	1	22
β-strand	146	1	22
α-helix	151-158	8
β-strand	164-168	5	21
β-strand	184-192	9	20
β-strand	207-218	12	23
β-strand	225-227	3	24
β-strand	237-240	4	24
β-strand	249-253	5	24
α-helix	256-261	6
β-strand	266-269	4	24
β-strand	274	1	25
β-strand	280-281	2	26
β-strand	285-289	5	26
β-strand	290	1	25
β-strand	295-300	6	26
β-strand	305-311	7	26
β-strand	315	1	27
β-strand	323	1	28
β-strand	326	1	28
β-strand	332-335	4	29
β-strand	340-345	6	29
β-strand	346	1	27
β-strand	352-358	7	29
β-strand	365-374	10	29
α-helix	375-377	3
β-strand	380-384	5	30
β-strand	387-392	6	30
β-strand	406-412	7	30
β-strand	418-424	7	30
β-strand	432-438	7	23
β-strand	443-448	6	23
β-strand	451-459	9	23

Chain D: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	206-218	13	31
β-strand	224-227	4	32
β-strand	237-241	5	32
β-strand	249-253	5	32
α-helix	256-261	6
β-strand	266-269	4	32
β-strand	274	1	33
β-strand	280-281	2	34
β-strand	285-288	4	34
α-helix	289	1
β-strand	290	1	33
β-strand	297-300	4	34
β-strand	305-309	5	34
β-strand	315	1	35
β-strand	323	1	36
β-strand	326	1	36
β-strand	332-335	4	37
β-strand	340-345	6	37
β-strand	346	1	35
β-strand	352-358	7	37
β-strand	365-374	10	37
α-helix	375-377	3
β-strand	380-384	5	38
β-strand	387-392	6	38
α-helix	394-395	2
β-strand	406-412	7	38
β-strand	418-419	2	38
β-strand	423-424	2	38
α-helix	425-426	2
β-strand	432-438	7	31
β-strand	443-448	6	31
β-strand	451-460	10	31

Chain E: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	48-49	2
β-strand	50	1	13
β-strand	53-56	4	39
α-helix	57-61	5
β-strand	62-63	2	40
β-strand	64	1	41
β-strand	67	1	41
β-strand	71-76	6	39
β-strand	80-85	6	42
β-strand	88-89	2	42
α-helix	90-91	2
α-helix	92-94	3
β-strand	96-101	6	39
β-strand	108-114	7	39
α-helix	118-122	5
β-strand	131-137	7	42
β-strand	142-144	3	42
β-strand	148-149	2	42
β-strand	151-152	2	40
β-strand	154-155	2	43
β-strand	161	1	44
α-helix	162-165	4
β-strand	167-169	3	45
β-strand	174-177	4	46
β-strand	179	1	44
α-helix	180-182	3
β-strand	183-184	2	43
β-strand	188-193	6	47
β-strand	197	1	47
β-strand	206-208	3	46
β-strand	213-216	4	46
β-strand	225-232	8	47
β-strand	237-239	3	47
α-helix	241-242	2
β-strand	243-245	3	47
β-strand	246-248	3	45
β-strand	249	1	48
α-helix	253-256	4
α-helix	258-261	4
β-strand	267-274	8	1
α-helix	281-282	2
β-strand	283	1	48
α-helix	286-290	5
β-strand	294-301	8	1

Chain F: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	41-43	3	49
β-strand	46-48	3	49
β-strand	67-69	3	49
α-helix	83-86	4
β-strand	92-94	3	49
β-strand	102	1	50
α-helix	103-104	2
β-strand	113-115	3	49
β-strand	123	1	50
β-strand	124	1	51
α-helix	126-131	6
β-strand	137-139	3	49
β-strand	150	1	51
α-helix	155-157	3
β-strand	163-165	3	49
β-strand	184-186	3	49
β-strand	195	1	52
α-helix	197-200	4
β-strand	208-210	3	49
β-strand	221	1	52
α-helix	226-228	3
β-strand	234-236	3	49
α-helix	245-246	2
β-strand	256-258	3	49
α-helix	269-271	3
β-strand	280-282	3	49
β-strand	304-306	3	49
β-strand	312-313	2	53
α-helix	316-318	3
α-helix	319-326	8
β-strand	333-335	3	49
β-strand	338	1	54
β-strand	339-341	3	53
β-strand	349	1	54

Chain G: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	99-104	6	55
β-strand	109-112	4	56
α-helix	117	1
β-strand	118-127	10	55
β-strand	128	1	57
β-strand	146	1	57
α-helix	151-158	8
β-strand	164-167	4	56
β-strand	184-192	9	55
β-strand	206-218	13	58
β-strand	224-228	5	59
β-strand	237-241	5	59
β-strand	249-253	5	59
α-helix	256-261	6
β-strand	266-269	4	59
β-strand	274-281	8	60
β-strand	285-290	6	60
β-strand	295-300	6	60
β-strand	305-311	7	60
β-strand	315	1	61
β-strand	332-335	4	62
β-strand	340-345	6	62
β-strand	346	1	61
β-strand	352-358	7	62
β-strand	365-374	10	62
α-helix	375-377	3
β-strand	380-384	5	63
β-strand	387-392	6	63
β-strand	406-412	7	63
β-strand	418-419	2	63
β-strand	423-424	2	63
β-strand	432-438	7	58
β-strand	443-448	6	58
β-strand	451-460	10	58

Chain H: 2 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	206-218	13	64
β-strand	224-227	4	65
β-strand	237-241	5	65
β-strand	249-253	5	65
α-helix	256-261	6
β-strand	266-269	4	65
β-strand	274	1	66
β-strand	280-281	2	67
β-strand	285-289	5	67
β-strand	290	1	66
β-strand	295-300	6	67
β-strand	305-311	7	67
β-strand	315	1	68
β-strand	323	1	69
β-strand	326	1	69
β-strand	332-335	4	70
β-strand	340-345	6	70
β-strand	346	1	68
β-strand	352-358	7	70
β-strand	365-374	10	70
β-strand	380-384	5	71
β-strand	387-392	6	71
β-strand	406-412	7	71
β-strand	418-419	2	71
β-strand	423-424	2	71
α-helix	425-426	2
β-strand	432-438	7	64
β-strand	443-448	6	64
β-strand	451-460	10	64

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Netrin receptor UNC5D	A, E	protein	285	RATTUS NORVEGICUS	F1LW30 (AlphaFold model)
Leucine-rich repeat transmembrane protein FLRT2	B, F	protein	339	MUS MUSCULUS	Q8BLU0 (AlphaFold model)
Adhesion G protein-coupled receptor L3	C, D, G, H	protein	383	MUS MUSCULUS	Q80TS3 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5FTT_1 NETRIN RECEPTOR UNC5D (chains A, E)
RGADSGEVLPDSIPSAPGTLPHFIEEPEDAYIIKSNPIALRCKARPAMQIFFKCNGEWVH
QNEHVSEESLDESSGLKVREVFINVTRQQVEDFHGPEDYWCQCVAWSHLGTSKSRKASVR
IAYLRKNFEQDPQGREVPIEGMIVLHCRPPEGVPAAEVEWLKNEEPIDSEQDENIDTRAD
HNLIIRQARLSDSGNYTCMAANIVAKRRSLSATVVVYVNGGWSSWTEWSACNVRCGRGWQ
KRSRTCTNPAPLNGGAFCEGMSVQKITCTALCPVDGGTKHHHHHH

Sequence of entity 2 (B, F), FASTA

>5FTT_2 LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 (chains B, F)
TGACPSVCRCDRNFVYCNERSLTSVPLGIPEGVTVLYLHNNQINNAGFPAELHNVQSVHT
VYLYGNQLDEFPMNLPKNVRVLHLQENNIQTISRAALAQLLKLEELHLDDNSISTVGVED
GAFREAISLKLLFLSKNHLSSVPVGLPVDLQELRVDENRIAVISDMAFQNLTSLERLIVD
GNLLTNKGIAEGTFSHLTKLKEFSIVRNSLSHPPPDLPGTHLIRLYLQDNQINHIPLTAF
ANLRKLERLDISNNQLRMLTQGVFDHLSNLKQLTARNNPWFCDCSIKWVTEWLKYIPSSL
NVRGFMCQGPEQVRGMAVRELNMNLLSCPTRTKHHHHHH

Sequence of entity 3 (C, D, G, H), FASTA

>5FTT_3 ADHESION G PROTEIN-COUPLED RECEPTOR L3 (chains C, D, G, H)
TGPIPMAVVRRELSCESYPIELRCPGTDVIMIESANYGRTDDKICDSDPAQMENIRCYLP
DAYKIMSQRCNNRTQCAVVAGPDVFPDPCPGTYKYLEVQYECVPYKVEQKVFLCPGLLKG
VYQSEHLFESDHQSGAWCKDPLQASDKIYYMPWTPYRTDTLTEYSSKDDFIAGRPTTTYK
LPHRVDGTGFVVYDGALFFNKERTRNIVKFDLRTRIKSGEAIIANANYHDTSPYRWGGKS
DIDLAVDENGLWVIYATEQNNGKIVISQLNPYTLRIEGTWDTAYDKRSASNAFMICGILY
VVKSVYEDDDNEATGNKIDYIYNTDQSKDSLVDVPFPNSYQYIAAVDYNPRDNLLYVWNN
YHVVKYSLDFGPLDGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (NA) are not listed.

Primary citation

Super-Complexes of Adhesion Gpcrs and Neural Guidance Receptors. Jackson, V.A., Mehmood, S., Chavent, M. et al. Nat Commun (2016) 7:11184. DOI 10.1038/NCOMMS11184 · PubMed

Other PDB entries of the same protein (UniProt F1LW30 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V2B 2.0 Å, rat Unc5D Ig domain 1
4V2C 4.0 Å, mouse FLRT2 LRR domain in complex with rat Unc5D Ig1 domain
7ZA3 4.0 Å, GPC3-Unc5D octamer structure and role in cell migration
7ZA1 4.1 Å, GPC3-Unc5D octamer structure and role in cell migration
7ZA2 4.6 Å, GPC3-Unc5D octamer structure and role in cell migration
5FTU 6.01 Å, Tetrameric complex of Latrophilin 3, Unc5D and FLRT2

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