5GJE: PDB entry 5GJE

Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1. Determined by electron microscopy at 21.0 Å resolution. Released 18 Jan 2017.

Method: Electron microscopy
Resolution: 21.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,506
Mol. weight: 151.67 kDa
Ligands: PO4, NAG
Released: 18 Jan 2017

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

Secondary structure: helices and β-sheets

5GJE contains 18 α-helices and 126 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, 60 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	9	1	2
β-strand	12-15	4	1
β-strand	25	1	1
β-strand	34-40	7	2
β-strand	45-50	6	2
β-strand	55-60	6	2
β-strand	67-71	5	2
β-strand	80-84	5	3
β-strand	89-94	6	3
β-strand	99-104	6	3
β-strand	111-114	4	3
β-strand	121-127	7	4
β-strand	132-137	6	4
β-strand	143-148	6	4
β-strand	155-158	4	4
β-strand	165-171	7	5
β-strand	176-181	6	5
β-strand	188-189	2	6
β-strand	190-191	2	5
β-strand	198-199	2	6
β-strand	211-213	3	7
β-strand	217-222	6	7
β-strand	227-232	6	7
β-strand	252-254	3	1
α-helix	257-259	3
β-strand	277-280	4	8
β-strand	287-290	4	8
β-strand	297	1	9
β-strand	304	1	9
β-strand	310-316	7	10
β-strand	320-324	5	10
β-strand	335-336	2	10
β-strand	343-349	7	11
β-strand	354-359	6	11
β-strand	364-368	5	11
β-strand	376-379	4	11
β-strand	388-392	5	12
β-strand	397-402	6	12
β-strand	407-412	6	12
β-strand	419-423	5	12
β-strand	428-435	8	13
β-strand	440-446	7	13
β-strand	451-456	6	13
β-strand	463-466	4	13
β-strand	473-476	4	14
β-strand	479	1	15
α-helix	480-482	3
β-strand	484	1	15
β-strand	487-489	3	14
β-strand	494-497	4	14
β-strand	499	1	15
β-strand	506-510	5	14
β-strand	519-522	4	16
β-strand	525-529	5	16
β-strand	536-540	5	16
β-strand	548-550	3	16
β-strand	556-563	8	10
α-helix	572-574	3
α-helix	576-579	4
β-strand	583-585	3	17
β-strand	592-594	3	17
β-strand	600-601	2	18
β-strand	608-609	2	18

Chain B: 10 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	633-638	6	19
β-strand	639	1	20
β-strand	641-645	5	19
β-strand	654-655	2	19
β-strand	664-670	7	20
β-strand	675-680	6	20
β-strand	685-690	6	20
β-strand	697-700	4	20
β-strand	709-713	5	21
β-strand	718-723	6	21
β-strand	728-733	6	21
β-strand	740-743	4	21
β-strand	750-756	7	22
β-strand	761-766	6	22
β-strand	772-777	6	22
β-strand	784-787	4	22
β-strand	793-799	7	23
β-strand	804-809	6	23
β-strand	814-819	6	23
β-strand	826-829	4	23
β-strand	835-841	7	24
β-strand	844-849	6	24
β-strand	854-859	6	24
β-strand	867-871	5	24
β-strand	879-882	4	19
α-helix	884-886	3
α-helix	892-894	3
α-helix	896-899	4
β-strand	903-906	4	25
β-strand	912-915	4	25
α-helix	920	1
β-strand	921-922	2	26
α-helix	923	1
β-strand	929-930	2	26
β-strand	935-940	6	27
β-strand	944-947	4	27
α-helix	954-956	3
β-strand	957-958	2	27
β-strand	967-973	7	28
β-strand	978-983	6	28
β-strand	988-992	5	28
β-strand	1000-1003	4	28
β-strand	1016-1022	7	29
β-strand	1027-1032	6	29
β-strand	1037-1042	6	29
β-strand	1047-1053	7	29
β-strand	1059-1065	7	30
β-strand	1070-1077	8	30
β-strand	1080-1087	8	30
β-strand	1094-1097	4	30
β-strand	1104-1110	7	31
β-strand	1115-1120	6	31
β-strand	1125-1130	6	31
β-strand	1137-1140	4	31
β-strand	1147-1153	7	32
β-strand	1156-1161	6	32
β-strand	1166-1171	6	32
α-helix	1177-1178	2
β-strand	1179-1182	4	32
β-strand	1188-1194	7	27
α-helix	1195-1197	3
α-helix	1199-1203	5
α-helix	1210-1213	4
β-strand	1217-1220	4	33
β-strand	1226-1229	4	33

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	183	1	34
β-strand	188	1	35
α-helix	192-194	3
β-strand	195	1	34
β-strand	199-204	6	35
β-strand	207-212	6	35
α-helix	213	1
β-strand	214	1	36
β-strand	219	1	37
α-helix	226-231	6
β-strand	234	1	35
α-helix	235-238	4
β-strand	239	1	36
β-strand	243-247	5	37
β-strand	261-265	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A	protein	611	Homo sapiens	O75581 (AlphaFold model)
Low-density lipoprotein receptor-related protein 6	B	protein	616	Homo sapiens	O75581 (AlphaFold model)
Dickkopf-related protein 1	C	protein	85	Homo sapiens	O94907 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GJE_1 Low-density lipoprotein receptor-related protein 6 (chains A)
APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTE
FNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQ
PRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKLYWA
DAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLR
EIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLEN
GKTCKDGATELLLLARRTDLRRISLDTPDFTDIVLQLEDIRHAIAIDYDPVEGYIYWTDD
EVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYWTDTGTDRIEVTRLNGTMRKI
LISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGWPNGLALDY
DEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQRRSIERVH
KRSAEREVIIDQLPDLMGLKATNVHRVIGSNPCAEENGGCSHLCLYRPQGLRCACPIGFE
LISDMKTCIVP

Sequence of entity 2 (B), FASTA

>5GJE_2 Low-density lipoprotein receptor-related protein 6 (chains B)
EAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAF
MNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSP
RALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDL
DTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQ
GHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCS
APTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIR
KAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGV
VLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALD
SRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKI
DMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSC
PMHLVLLQDELSCGEP

Sequence of entity 3 (C), FASTA

>5GJE_3 Dickkopf-related protein 1 (chains C)
KGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGE
GLSCRIQKDHHQASNSSRLHTCQRH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1. Matoba, K., Mihara, E., Tamura-Kawakami, K. et al. Cell Rep (2017) 18:32-40. DOI 10.1016/j.celrep.2016.12.017 · 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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