7ZA3: Glypican-3

GPC3-Unc5D octamer structure and role in cell migration. Determined by X-ray diffraction at 4.0 Å resolution. Released 2 Nov 2022.

Method: X-ray diffraction
Resolution: 4.0 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 8
Atoms: 19,445
Mol. weight: 338.39 kDa
Ligands: NAG, MAN
Released: 2 Nov 2022

Explore 7ZA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZA3 contains 113 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.

Chain A: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	74-132	59
α-helix	134-136	3
α-helix	139-155	17
α-helix	162-177	16
α-helix	178-182	5
α-helix	194-203	10
α-helix	210-243	34
α-helix	249-259	11
α-helix	261-264	4
β-strand	272	1	1
β-strand	273	1	2
α-helix	274-284	11
α-helix	286-289	4
α-helix	292-306	15
α-helix	316-335	20
α-helix	337-347	11
α-helix	383-394	12
α-helix	395-397	3
α-helix	404-411	8
β-strand	415	1	2
β-strand	419-422	4	1
β-strand	427-430	4	1
α-helix	456-475	20

Chain B: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	74-132	59
α-helix	134-136	3
α-helix	139-155	17
α-helix	162-177	16
α-helix	178-182	5
α-helix	194-203	10
α-helix	210-242	33
α-helix	249-259	11
α-helix	261-264	4
β-strand	272	1	3
β-strand	273	1	4
α-helix	274-284	11
α-helix	286-289	4
α-helix	292-306	15
α-helix	316-335	20
α-helix	337-347	11
α-helix	383-394	12
α-helix	395-397	3
α-helix	404-411	8
β-strand	415	1	4
β-strand	419-422	4	3
β-strand	427-430	4	3
α-helix	456-475	20

Chain C: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	74-132	59
α-helix	134-136	3
α-helix	139-155	17
α-helix	162-177	16
α-helix	178-182	5
α-helix	194-203	10
α-helix	210-242	33
α-helix	249-259	11
α-helix	261-264	4
β-strand	272	1	5
β-strand	273	1	6
α-helix	274-284	11
α-helix	286-289	4
α-helix	291-306	16
α-helix	316-335	20
α-helix	337-347	11
α-helix	383-394	12
α-helix	395-397	3
α-helix	404-411	8
β-strand	415	1	6
β-strand	419-422	4	5
β-strand	427-430	4	5
α-helix	456-474	19

Chain D: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	74-132	59
α-helix	134-136	3
α-helix	139-155	17
α-helix	162-177	16
α-helix	178-182	5
α-helix	194-203	10
α-helix	210-242	33
α-helix	249-259	11
α-helix	261-264	4
β-strand	272	1	7
β-strand	273	1	8
α-helix	274-284	11
α-helix	286-289	4
α-helix	291-306	16
α-helix	316-335	20
α-helix	337-347	11
α-helix	383-394	12
α-helix	395-397	3
α-helix	404-411	8
β-strand	415	1	8
β-strand	419-422	4	7
β-strand	427-430	4	7
α-helix	456-475	20

Chain E: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	9
α-helix	57-61	5
β-strand	62-63	2	10
β-strand	64	1	11
β-strand	67	1	11
β-strand	71-76	6	9
β-strand	80-85	6	12
β-strand	88-89	2	12
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	9
β-strand	108-114	7	9
α-helix	118-123	6
β-strand	131-137	7	12
β-strand	142-144	3	12
β-strand	148-149	2	12
β-strand	151-152	2	10
β-strand	155	1	13
β-strand	161	1	14
α-helix	162-165	4
β-strand	167-168	2	15
β-strand	174-177	4	16
β-strand	179	1	14
α-helix	180-181	2
β-strand	183	1	13
β-strand	188-193	6	17
β-strand	197	1	17
β-strand	206-208	3	16
β-strand	213-216	4	16
β-strand	225-232	8	17
β-strand	237-239	3	17
α-helix	241-242	2
β-strand	243-245	3	17
β-strand	246-247	2	15
β-strand	249	1	18
α-helix	253-256	4
α-helix	258-261	4
β-strand	268-274	7	19
α-helix	281-282	2
β-strand	283	1	18
α-helix	286-290	5
β-strand	294-300	7	19

Chain F: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	20
α-helix	57-59	3
β-strand	62-63	2	21
β-strand	64	1	22
β-strand	67	1	22
β-strand	71-76	6	20
β-strand	80-85	6	23
β-strand	88-89	2	23
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	20
β-strand	108-114	7	20
α-helix	118-122	5
β-strand	131-137	7	23
β-strand	142-144	3	23
β-strand	148-149	2	23
β-strand	151-152	2	21
β-strand	155	1	24
β-strand	161	1	25
α-helix	162-165	4
β-strand	167-168	2	26
β-strand	174-177	4	27
β-strand	179	1	25
α-helix	180-181	2
β-strand	183	1	24
β-strand	188-193	6	28
β-strand	197	1	28
β-strand	206-208	3	27
β-strand	213-216	4	27
β-strand	225-232	8	28
β-strand	237-239	3	28
α-helix	241-242	2
β-strand	243-245	3	28
β-strand	246-247	2	26
β-strand	249	1	29
α-helix	258-261	4
β-strand	268-274	7	30
α-helix	281-282	2
β-strand	283	1	29
α-helix	286-290	5
β-strand	294-300	7	30

Chain G: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	31
α-helix	57-61	5
β-strand	62-63	2	32
β-strand	64	1	33
β-strand	67	1	33
β-strand	71-76	6	31
β-strand	80-85	6	34
β-strand	88-89	2	34
α-helix	90-91	2
α-helix	92-94	3
β-strand	96-101	6	31
β-strand	108-114	7	31
α-helix	118-122	5
β-strand	131-137	7	34
β-strand	142-144	3	34
β-strand	148-149	2	34
β-strand	151-152	2	32
β-strand	154-155	2	35
β-strand	161	1	36
α-helix	162-165	4
β-strand	167-168	2	37
β-strand	174-177	4	38
β-strand	179	1	36
α-helix	180-181	2
β-strand	183-184	2	35
β-strand	188-193	6	39
β-strand	197	1	39
β-strand	206-208	3	38
β-strand	213-216	4	38
β-strand	225-232	8	39
β-strand	237-239	3	39
α-helix	241-242	2
β-strand	243-245	3	39
β-strand	246-247	2	37
β-strand	249	1	40
α-helix	258-261	4
β-strand	268-274	7	41
α-helix	281-282	2
β-strand	283	1	40
α-helix	286-290	5
β-strand	294-300	7	41

Chain H: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	42
α-helix	57-61	5
β-strand	62-63	2	43
β-strand	64	1	44
β-strand	67	1	44
β-strand	71-76	6	42
β-strand	80-85	6	45
β-strand	88-89	2	45
α-helix	90-91	2
α-helix	92-94	3
β-strand	95-101	7	42
β-strand	108-114	7	42
α-helix	118-122	5
β-strand	131-137	7	45
β-strand	142-144	3	45
β-strand	148-149	2	45
β-strand	151-152	2	43
β-strand	154-155	2	46
β-strand	161	1	47
α-helix	162-165	4
β-strand	167-168	2	48
β-strand	174-177	4	49
β-strand	179	1	47
α-helix	180-181	2
β-strand	183-184	2	46
β-strand	188-193	6	50
β-strand	197	1	50
β-strand	206-208	3	49
β-strand	213-216	4	49
β-strand	225-232	8	50
β-strand	237-239	3	50
α-helix	241-242	2
β-strand	243-245	3	50
β-strand	246-247	2	48
β-strand	249	1	51
α-helix	258-261	4
β-strand	268-274	7	52
α-helix	281-282	2
β-strand	283	1	51
α-helix	286-290	5
β-strand	294-300	7	52

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glypican-3	A, B, C, D	protein	464	Mus musculus	Q8CFZ4 (AlphaFold model)
Netrin receptor UNC5D	E, F, G, H	protein	268	Rattus norvegicus	F1LW30 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7ZA3_1 Glypican-3 (chains A, B, C, D)
ETGDATCHQVRSFFQRLQPGLKWVPETPVPGSDLQVCLPKGPTCCSRKMEEKYQLTARLN
MEQLLQSASMELKFLIIQNAAVFQEAFEIVVRHAKNYTNAMFKNNYPSLTPQAFEFVGEF
FTDVSLYILGSDINVDDMVNELFDSLFPVIYTQMMNPGLPESVLDINECLRGARRDLKVF
GSFPKLIMTQVSKSLQVTRIFLQALNLGIEVINTTDHLKFSKDCGRMLTRMWYCSYCQGL
MMVKPCGGYCNVVMQGCMAGVVEIDKYWREYILSLEELVNGMYRIYDMENVLLGLFSTIH
DSIQYVQKNGGKLTTTIGKLCAHSQQRQYRSAYYPEDLFIDKKILKVAHVEHEETLSSRR
RELIQKLKSFINFYSALPGYICSHSPVAENDTLCWNGQELVERYSQKAARNGMKNQFNLH
ELKMKGPEPVVSQIIDKLKHINQLLRTMSVPKGKVGTKHHHHHH

Sequence of entity 2 (E, F, G, H), FASTA

>7ZA3_2 Netrin receptor UNC5D (chains E, F, G, H)
SAPGTLPHFIEEPEDAYIIKSNPIALRCKARPAMQIFFKCNGEWVHQNEHVSEESLDESS
GLKVREVFINVTRQQVEDFHGPEDYWCQCVAWSHLGTSKSRKASVRIAYLRKNFEQDPQG
REVPIEGMIVLHCRPPEGVPAAEVEWLKNEEPIDSEQDENIDTRADHNLIIRQARLSDSG
NYTCMAANIVAKRRSLSATVVVYVNGGWSSWTEWSACNVRCGRGWQKRSRTCTNPAPLNG
GAFCEGMSVQKITCTALCPVDGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14
MAN	alpha-D-mannopyranose	C6 H12 O6	3

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 Q8CFZ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZAV 2.9 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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