3S8V: LRP6-Dkk1 complex

Crystal structure of LRP6-Dkk1 complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,177
Mol. weight: 151.43 kDa
Released: 26 Oct 2011

Explore 3S8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S8V contains 12 α-helices and 123 β-strands across 3 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: 4 helices, 58 β-strands

Element	Residues	Length	Sheet
β-strand	633-637	5	1
β-strand	639	1	2
β-strand	642-646	5	1
β-strand	653-655	3	1
β-strand	664-670	7	2
β-strand	675-680	6	2
β-strand	685-690	6	2
β-strand	697-700	4	2
β-strand	707-713	7	3
β-strand	718-723	6	3
β-strand	728-733	6	3
β-strand	740-743	4	3
β-strand	750-756	7	4
β-strand	761-766	6	4
β-strand	772-777	6	4
β-strand	784-787	4	4
β-strand	793	1	5
β-strand	797-799	3	5
β-strand	804-809	6	5
β-strand	814-819	6	5
β-strand	826-829	4	5
β-strand	835-840	6	6
β-strand	844-849	6	6
β-strand	854-859	6	6
β-strand	867-870	4	6
β-strand	877-882	6	1
α-helix	892-894	3
α-helix	896-899	4
β-strand	903-906	4	7
β-strand	912-915	4	7
β-strand	921-922	2	8
β-strand	929-930	2	8
β-strand	935-939	5	9
β-strand	944-948	5	9
β-strand	957-958	2	9
β-strand	966-973	8	10
β-strand	978-984	7	10
β-strand	988-992	5	10
β-strand	1000-1003	4	10
β-strand	1016-1022	7	11
β-strand	1027-1032	6	11
β-strand	1037-1042	6	11
β-strand	1047-1052	6	11
β-strand	1059-1065	7	12
β-strand	1070-1075	6	12
β-strand	1082-1087	6	12
β-strand	1094-1097	4	12
β-strand	1104-1110	7	13
β-strand	1115-1120	6	13
β-strand	1125-1130	6	13
β-strand	1137-1140	4	13
β-strand	1147-1152	6	14
β-strand	1156-1161	6	14
β-strand	1166-1171	6	14
β-strand	1179-1182	4	14
β-strand	1190-1194	5	9
α-helix	1199-1203	5
α-helix	1210-1213	4
β-strand	1217-1218	2	15
β-strand	1221	1	16
β-strand	1225	1	16
β-strand	1228-1229	2	15

Chain B: 5 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	633-637	5	17
β-strand	642-646	5	17
β-strand	653-655	3	17
β-strand	664-670	7	18
β-strand	675-680	6	18
β-strand	685-690	6	18
β-strand	697-700	4	18
β-strand	709-713	5	19
β-strand	718-723	6	19
β-strand	728-733	6	19
β-strand	740-743	4	19
β-strand	750-756	7	20
β-strand	761-766	6	20
β-strand	769	1	21
β-strand	772-777	6	20
β-strand	784-787	4	20
β-strand	793	1	22
β-strand	797-799	3	22
β-strand	804-809	6	22
β-strand	814-819	6	22
β-strand	826-829	4	22
β-strand	835-840	6	23
β-strand	844-849	6	23
β-strand	854-859	6	23
β-strand	867-870	4	23
β-strand	879-882	4	17
α-helix	892-894	3
α-helix	896-899	4
β-strand	903-906	4	24
β-strand	912-915	4	24
β-strand	921-922	2	25
β-strand	929-930	2	25
β-strand	935-940	6	26
β-strand	943-947	5	26
α-helix	954-956	3
β-strand	957-958	2	26
β-strand	967-973	7	27
β-strand	978-983	6	27
β-strand	988-992	5	27
β-strand	1000-1003	4	27
β-strand	1016-1022	7	28
β-strand	1027-1032	6	28
β-strand	1037-1042	6	28
β-strand	1047-1053	7	28
β-strand	1059-1065	7	29
β-strand	1070-1077	8	29
β-strand	1080-1087	8	29
β-strand	1094-1097	4	29
β-strand	1104-1110	7	30
β-strand	1115-1120	6	30
β-strand	1125-1130	6	30
β-strand	1137-1140	4	30
β-strand	1147-1152	6	31
β-strand	1156-1161	6	31
β-strand	1166-1171	6	31
β-strand	1179-1182	4	31
β-strand	1188-1194	7	26
α-helix	1199-1203	5
α-helix	1210-1213	4
β-strand	1217-1220	4	32
β-strand	1226-1229	4	32

Chain X: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	188	1	33
α-helix	192-194	3
β-strand	199-204	6	33
β-strand	207-212	6	33
α-helix	213	1
β-strand	214	1	34
β-strand	219	1	21
α-helix	228-231	4
β-strand	234	1	33
β-strand	239	1	34
β-strand	245-247	3	21
β-strand	261-263	3	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A, B	protein	623	Homo sapiens	O75581 (AlphaFold model)
Dickkopf-related protein 1	X	protein	88	Homo sapiens	O94907 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3S8V_1 Low-density lipoprotein receptor-related protein 6 (chains A, B)
HHHHHHHHVPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTD
ISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQ
VLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDY
AKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANK
TSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHY
SLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLY
WIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINV
TRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSG
LSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWI
DKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLV
KGDGTTRCSCPMHLVLLQDELSC

Sequence of entity 2 (X), FASTA

>3S8V_2 Dickkopf-related protein 1 (chains X)
GPGSGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCY
CGEGLSCRIQKDHHQASNSSRLHTCQRH

Primary citation

Crystal structures of the extracellular domain of LRP6 and its complex with DKK1. Cheng, Z., Biechele, T., Wei, Z. et al. Nat Struct Mol Biol (2011) 18:1204-1210. DOI 10.1038/nsmb.2139 · PubMed

Other PDB entries of the same protein (UniProt O75581 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SOV 1.27 Å, The structure of a beta propeller domain in complex with peptide S
7NAM 1.6 Å, LRP6_E1 in complex with Lr-EET-3.5
8FFE 1.72 Å, Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide
3SOB 1.9 Å, The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB
3SOQ 1.9 Å, The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1…
4A0P 1.9 Å, Crystal structure of LRP6P3E3P4E4
8DVM 2.0 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6
4NM5 2.3 Å, Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif
4NM7 2.3 Å, Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif
8DVL 2.5 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18
5AIR 2.53 Å, Structural analysis of mouse GSK3beta fused with LRP6 peptide.
8DVN 2.53 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10

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