7ZA1: Netrin receptor UNC5D

GPC3-Unc5D octamer structure and role in cell migration. Determined by X-ray diffraction at 4.1 Å resolution. Released 2 Nov 2022.

Method: X-ray diffraction
Resolution: 4.1 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 8
Atoms: 19,646
Mol. weight: 341.72 kDa
Ligands: NAG, MAN
Released: 2 Nov 2022

Explore 7ZA1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZA1 contains 109 α-helices and 144 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.

Chains A, B, C and D: 17 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	75-133	59
α-helix	135-137	3
α-helix	140-156	17
α-helix	163-178	16
α-helix	179-183	5
α-helix	195-204	10
α-helix	211-243	33
α-helix	250-260	11
α-helix	262-265	4
β-strand	273	1	45
β-strand	274	1	46
α-helix	275-285	11
α-helix	287-290	4
α-helix	292-307	16
α-helix	316-335	20
α-helix	338-348	11
α-helix	384-396	13
α-helix	405-411	7
β-strand	416	1	46
β-strand	422-423	2	45
β-strand	428-429	2	45
α-helix	457-476	20

Chain E: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	1
α-helix	57-61	5
β-strand	62-63	2	2
β-strand	64	1	3
β-strand	67	1	3
β-strand	71-76	6	1
β-strand	80-85	6	4
β-strand	88-89	2	4
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	1
β-strand	108-114	7	1
α-helix	118-122	5
β-strand	131-137	7	4
β-strand	142-144	3	4
β-strand	148-149	2	4
β-strand	151-152	2	2
β-strand	155	1	5
β-strand	161	1	6
α-helix	162-165	4
β-strand	167-168	2	7
β-strand	174-177	4	8
β-strand	179	1	6
α-helix	180-182	3
β-strand	183	1	5
β-strand	188-193	6	9
β-strand	197	1	9
β-strand	206-208	3	8
β-strand	213-216	4	8
β-strand	225-232	8	9
β-strand	237-239	3	9
α-helix	241-242	2
β-strand	243-245	3	9
β-strand	246-247	2	7
β-strand	249	1	10
α-helix	253-256	4
α-helix	258-261	4
β-strand	268-274	7	11
α-helix	281-282	2
β-strand	283	1	10
α-helix	286-290	5
β-strand	294-300	7	11

Chain F: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	12
α-helix	57-61	5
β-strand	62-63	2	13
β-strand	64	1	14
β-strand	67	1	14
β-strand	71-76	6	12
β-strand	80-85	6	15
β-strand	88-89	2	15
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	12
β-strand	108-114	7	12
α-helix	118-122	5
β-strand	131-137	7	15
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	151-152	2	13
β-strand	155	1	16
β-strand	161	1	17
α-helix	162-165	4
β-strand	167-168	2	18
β-strand	174-177	4	19
β-strand	179	1	17
α-helix	180-182	3
β-strand	183	1	16
β-strand	188-193	6	20
β-strand	197	1	20
β-strand	206-208	3	19
β-strand	213-216	4	19
β-strand	225-232	8	20
β-strand	237-239	3	20
α-helix	241-242	2
β-strand	243-245	3	20
β-strand	246-247	2	18
β-strand	249	1	21
α-helix	258-261	4
β-strand	268-274	7	22
α-helix	281-282	2
β-strand	283	1	21
α-helix	286-290	5
β-strand	294-300	7	22

Chain G: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	23
α-helix	57-61	5
β-strand	62-63	2	24
β-strand	64	1	25
β-strand	67	1	25
β-strand	71-76	6	23
β-strand	80-85	6	26
β-strand	88-89	2	26
α-helix	90-91	2
α-helix	92-94	3
β-strand	96-101	6	23
β-strand	108-114	7	23
α-helix	118-122	5
β-strand	131-137	7	26
β-strand	142-144	3	26
β-strand	148-149	2	26
β-strand	151-152	2	24
β-strand	154-155	2	27
β-strand	161	1	28
α-helix	162-165	4
β-strand	167-168	2	29
β-strand	174-177	4	30
β-strand	179	1	28
α-helix	180-182	3
β-strand	183-184	2	27
β-strand	188-193	6	31
β-strand	197	1	31
β-strand	206-208	3	30
β-strand	213-216	4	30
β-strand	225-232	8	31
β-strand	237-239	3	31
α-helix	241-242	2
β-strand	243-245	3	31
β-strand	246-247	2	29
β-strand	249	1	32
α-helix	258-261	4
β-strand	268-274	7	33
α-helix	281-282	2
β-strand	283	1	32
α-helix	286-290	5
β-strand	294-300	7	33

Chain H: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	34
α-helix	57-61	5
β-strand	62-63	2	35
β-strand	64	1	36
β-strand	67	1	36
β-strand	71-76	6	34
β-strand	80-85	6	37
β-strand	88-89	2	37
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	34
β-strand	108-114	7	34
α-helix	118-122	5
β-strand	131-137	7	37
β-strand	142-144	3	37
β-strand	148-149	2	37
β-strand	151-152	2	35
β-strand	154-155	2	38
β-strand	161	1	39
α-helix	162-165	4
β-strand	167-168	2	40
β-strand	174-177	4	41
β-strand	179	1	39
α-helix	180-182	3
β-strand	183-184	2	38
β-strand	188-193	6	42
β-strand	197	1	42
β-strand	206-208	3	41
β-strand	213-216	4	41
β-strand	225-232	8	42
β-strand	237-239	3	42
α-helix	241-242	2
β-strand	243-245	3	42
β-strand	246-247	2	40
β-strand	249	1	43
α-helix	258-261	4
β-strand	268-274	7	44
α-helix	281-282	2
β-strand	283	1	43
α-helix	286-290	5
β-strand	294-300	7	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Netrin receptor UNC5D	E, F, G, H	protein	268	Rattus norvegicus	F1LW30 (AlphaFold model)
Glypican-3	A, B, C, D	protein	464	Homo sapiens	P51654 (AlphaFold model)

Sequence of entity 1 (E, F, G, H), FASTA

>7ZA1_1 Netrin receptor UNC5D (chains E, F, G, H)
SAPGTLPHFIEEPEDAYIIKSNPIALRCKARPAMQIFFKCNGEWVHQNEHVSEESLDESS
GLKVREVFINVTRQQVEDFHGPEDYWCQCVAWSHLGTSKSRKASVRIAYLRKNFEQDPQG
REVPIEGMIVLHCRPPEGVPAAEVEWLKNEEPIDSEQDENIDTRADHNLIIRQARLSDSG
NYTCMAANIVAKRRSLSATVVVYVNGGWSSWTEWSACNVRCGRGWQKRSRTCTNPAPLNG
GAFCEGMSVQKITCTALCPVDGHHHHHH

Sequence of entity 2 (A, B, C, D), FASTA

>7ZA1_2 Glypican-3 (chains A, B, C, D)
ETGDATCHQVRSFFQRLQPGLKWVPETPVPGSDLQVCLPKGPTCCSRKMEEKYQLTARLN
MEQLLQSASMELKFLIIQNAAVFQEAFEIVVRHAKNYTNAMFKNNYPSLTPQAFEFVGEF
FTDVSLYILGSDINVDDMVNELFDSLFPVIYTQLMNPGLPDSALDINECLRGARRDLKVF
GNFPKLIMTQVSKSLQVTRIFLQALNLGIEVINTTDHLKFSKDCGRMLTRMWYCSYCQGL
MMVKPCGGYCNVVMQGCMAGVVEIDKYWREYILSLEELVNGMYRIYDMENVLLGLFSTIH
DSIQYVQKNAGKLTTTIGKLCAHSQQRQYRFAYYPEDLFIDKKVLKVAHVEHEETLSSRR
RELIQKLKSFISFYSALPGYICSHSPVAENDTLCWNGQELVERYSQKAARNGMKNQFNLH
ELKMKGPEPVVSQIIDKLKHINQLLRTMSMPKGRVGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
MAN	alpha-D-mannopyranose	C6 H12 O6	6

Primary citation

GPC3-Unc5 receptor complex structure and role in cell migration. Akkermans, O., Delloye-Bourgeois, C., Peregrina, C. et al. Cell (2022) 185:3931-3949.e26. DOI 10.1016/j.cell.2022.09.025 · 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
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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