5FTU: Netrin receptor UNC5D

Tetrameric complex of Latrophilin 3, Unc5D and FLRT2. Determined by X-ray diffraction at 6.01 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 6.01 Å
Organisms: RATTUS NORVEGICUS, MUS MUSCULUS
Chains: 12
Atoms: 25,680
Mol. weight: 428.82 kDa
Ligands: NAG, CA
Released: 4 May 2016

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

Secondary structure: helices and β-sheets

5FTU contains 52 α-helices and 280 β-strands across 12 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.

Chains A and E: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	47-49	3
β-strand	53-56	4	1
α-helix	57-61	5
β-strand	64	1	2
β-strand	67	1	2
β-strand	69-76	8	1
β-strand	81-85	5	3
β-strand	88-89	2	3
α-helix	90-91	2
β-strand	96-98	3	1
α-helix	100-102	3
β-strand	110-116	7	1
α-helix	118-122	5
β-strand	130-137	8	3
β-strand	142-144	3	3
β-strand	148-150	3	3

Chains B, F and J: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	4
β-strand	46-48	3	4
β-strand	67-69	3	4
α-helix	83-86	4
β-strand	92-94	3	4
β-strand	102	1	5
β-strand	113-115	3	4
β-strand	123	1	5
β-strand	124	1	6
α-helix	127-130	4
β-strand	137-139	3	4
β-strand	150	1	6
α-helix	154-157	4
β-strand	163-165	3	4
β-strand	184-186	3	4
β-strand	195	1	7
β-strand	208-210	3	4
β-strand	221	1	7
β-strand	234-236	3	4
α-helix	245-246	2
β-strand	256-258	3	4
β-strand	280-282	3	4
β-strand	304-306	3	4
β-strand	312-313	2	8
α-helix	319-326	8
β-strand	333-335	3	4
β-strand	338	1	9
β-strand	339-341	3	8
β-strand	349	1	9

Chain C: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	101	1	10
β-strand	104	1	10
β-strand	107-112	6	11
β-strand	118-127	10	10
β-strand	128	1	12
α-helix	138-141	4
β-strand	146	1	12
α-helix	151-158	8
β-strand	164-169	6	11
β-strand	184-192	9	10
α-helix	196-198	3
β-strand	207-218	12	13
β-strand	224-225	2	14
β-strand	228	1	15
β-strand	237	1	15
β-strand	240-241	2	14
β-strand	249-251	3	16
β-strand	253	1	15
α-helix	256-261	6
β-strand	267-269	3	16
α-helix	273	1
β-strand	274	1	17
β-strand	281	1	18
β-strand	285-289	5	18
β-strand	290	1	17
β-strand	295-300	6	18
β-strand	305-311	7	18
β-strand	315	1	19
β-strand	332-335	4	20
β-strand	340-345	6	20
β-strand	346	1	19
β-strand	352-358	7	20
β-strand	365-374	10	20
β-strand	380-384	5	21
β-strand	387-392	6	21
β-strand	406-412	7	21
β-strand	418-419	2	21
β-strand	423-424	2	21
α-helix	425-426	2
β-strand	432-438	7	13
β-strand	443-448	6	13
β-strand	451-459	9	13

Chains D, H and L: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	206-218	13	22
β-strand	224-228	5	23
β-strand	237-241	5	23
β-strand	249-253	5	23
α-helix	256-261	6
β-strand	266-269	4	23
β-strand	274	1	24
β-strand	280-281	2	25
β-strand	285-288	4	25
α-helix	289	1
β-strand	290	1	24
β-strand	297-300	4	25
β-strand	305-309	5	25
β-strand	315	1	26
β-strand	332-335	4	27
β-strand	340-345	6	27
β-strand	346	1	26
β-strand	352-358	7	27
β-strand	365-374	10	27
β-strand	380-384	5	28
β-strand	387-392	6	28
β-strand	406-412	7	28
β-strand	418-419	2	28
β-strand	423-424	2	28
α-helix	425-426	2
β-strand	432-438	7	22
β-strand	443-448	6	22
β-strand	451-460	10	22

Chains G and K: 4 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	101-104	4	38
β-strand	107-112	6	39
β-strand	118-127	10	38
β-strand	128	1	40
β-strand	146	1	40
α-helix	151-158	8
β-strand	164-169	6	39
β-strand	184-192	9	38
α-helix	196-198	3
β-strand	207-218	12	41
β-strand	224-228	5	42
β-strand	237-241	5	42
β-strand	249-253	5	42
α-helix	256-261	6
β-strand	266-269	4	42
β-strand	274	1	43
β-strand	280-281	2	44
β-strand	285-289	5	44
β-strand	290	1	43
β-strand	295-300	6	44
β-strand	305-311	7	44
β-strand	315	1	45
β-strand	332-335	4	46
β-strand	340-345	6	46
β-strand	346	1	45
β-strand	352-358	7	46
β-strand	365-374	10	46
β-strand	380-384	5	47
β-strand	387-392	6	47
β-strand	406-412	7	47
β-strand	418-419	2	47
β-strand	423-424	2	47
α-helix	425-426	2
β-strand	432-438	7	41
β-strand	443-448	6	41
β-strand	451-459	9	41

Chain I: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	47-49	3
β-strand	53-56	4	55
α-helix	57-61	5
β-strand	64	1	56
β-strand	67	1	56
β-strand	69-76	8	55
β-strand	81-85	5	57
β-strand	88-89	2	57
α-helix	90-91	2
β-strand	96-98	3	55
β-strand	110-116	7	55
α-helix	118-122	5
β-strand	130-137	8	57
β-strand	142-144	3	57
β-strand	148-150	3	57

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Netrin receptor UNC5D	A, E, I	protein	139	RATTUS NORVEGICUS	F1LW30 (AlphaFold model)
Leucine-rich repeat transmembrane protein FLRT2	B, F, J	protein	339	MUS MUSCULUS	Q8BLU0 (AlphaFold model)
Adhesion G protein-coupled receptor L3	C, D, G, H, K, L	protein	383	MUS MUSCULUS	Q80TS3 (AlphaFold model)

Sequence of entity 1 (A, E, I), FASTA

>5FTU_1 NETRIN RECEPTOR UNC5D (chains A, E, I)
RGADSGEVLPDSIPSAPGTLPHFIEEPEDAYIIKSNPIALRCKARPAMQIFFKCNGEWVH
QNEHVSEESLDESSGLKVREVFINVTRQQVEDFHGPEDYWCQCVAWSHLGTSKSRKASVR
IAYLRKNFEQGTKHHHHHH

Sequence of entity 2 (B, F, J), FASTA

>5FTU_2 LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 (chains B, F, J)
TGACPSVCRCDRNFVYCNERSLTSVPLGIPEGVTVLYLHNNQINNAGFPAELHNVQSVHT
VYLYGNQLDEFPMNLPKNVRVLHLQENNIQTISRAALAQLLKLEELHLDDNSISTVGVED
GAFREAISLKLLFLSKNHLSSVPVGLPVDLQELRVDENRIAVISDMAFQNLTSLERLIVD
GNLLTNKGIAEGTFSHLTKLKEFSIVRNSLSHPPPDLPGTHLIRLYLQDNQINHIPLTAF
ANLRKLERLDISNNQLRMLTQGVFDHLSNLKQLTARNNPWFCDCSIKWVTEWLKYIPSSL
NVRGFMCQGPEQVRGMAVRELNMNLLSCPTRTKHHHHHH

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

>5FTU_3 ADHESION G PROTEIN-COUPLED RECEPTOR L3 (chains C, D, G, H, K, L)
TGPIPMAVVRRELSCESYPIELRCPGTDVIMIESANYGRTDDKICDSDPAQMENIRCYLP
DAYKIMSQRCNNRTQCAVVAGPDVFPDPCPGTYKYLEVQYECVPYKVEQKVFLCPGLLKG
VYQSEHLFESDHQSGAWCKDPLQASDKIYYMPWTPYRTDTLTEYSSKDDFIAGRPTTTYK
LPHRVDGTGFVVYDGALFFNKERTRNIVKFDLRTRIKSGEAIIANANYHDTSPYRWGGKS
DIDLAVDENGLWVIYATEQNNGKIVISQLNPYTLRIEGTWDTAYDKRSASNAFMICGILY
VVKSVYEDDDNEATGNKIDYIYNTDQSKDSLVDVPFPNSYQYIAAVDYNPRDNLLYVWNN
YHVVKYSLDFGPLDGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
CA	Calcium ion	Ca	6

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
5FTT 3.4 Å, Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR)
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

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