8FFE: LRP6 E1E2 domains

Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide. Determined by X-ray diffraction at 1.72 Å resolution. Released 8 Mar 2023.

Method: X-ray diffraction
Resolution: 1.72 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,116
Mol. weight: 125.4 kDa
Ligands: SIN
Released: 8 Mar 2023

Explore 8FFE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FFE contains 29 α-helices and 101 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: 7 helices, 58 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	1
β-strand	28	1	2
β-strand	31-35	5	1
α-helix	42-43	2
β-strand	44-47	4	1
β-strand	53-59	7	2
α-helix	60-62	3
β-strand	64-69	6	2
β-strand	74-79	6	2
β-strand	87-90	4	2
β-strand	99-103	5	3
β-strand	108-113	6	3
β-strand	118-123	6	3
β-strand	130-133	4	3
β-strand	140-146	7	4
β-strand	151-156	6	4
β-strand	162-167	6	4
β-strand	174-177	4	4
β-strand	184-190	7	5
β-strand	195-200	6	5
β-strand	205-210	6	5
β-strand	217-221	5	5
β-strand	227-233	7	6
β-strand	236-241	6	6
β-strand	246-251	6	6
β-strand	259-262	4	6
β-strand	271-273	3	1
α-helix	276-278	3
α-helix	290-292	3
β-strand	296-299	4	7
β-strand	306-309	4	7
β-strand	316	1	8
β-strand	323	1	8
β-strand	329-334	6	9
β-strand	336	1	10
β-strand	339-343	5	9
β-strand	351-353	3	9
β-strand	362-368	7	10
β-strand	373-378	6	10
β-strand	383-387	5	10
β-strand	395-398	4	10
β-strand	407-411	5	11
β-strand	416-421	6	11
β-strand	426-431	6	11
β-strand	438-441	4	11
β-strand	448-454	7	12
β-strand	459-464	6	12
β-strand	470-475	6	12
β-strand	482-485	4	12
β-strand	492-498	7	13
β-strand	503-508	6	13
β-strand	513-518	6	13
β-strand	525-528	4	13
β-strand	535-541	7	14
β-strand	544-549	6	14
β-strand	554-559	6	14
β-strand	565-569	5	14
β-strand	578-582	5	9
α-helix	591-593	3
α-helix	595-598	4
β-strand	602-604	3	15
β-strand	611-613	3	15
β-strand	619-620	2	16
β-strand	627-628	2	16
α-helix	629-631	3

Chain H: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	227-230	4
α-helix	232-239	8
β-strand	1003-1007	5	17
β-strand	1010-1012	3	18
β-strand	1018-1025	8	17
α-helix	1029-1031	3
β-strand	1034-1039	6	18
β-strand	1045-1052	8	18
β-strand	1056-1059	4	18
β-strand	1067-1072	6	17
α-helix	1073-1075	3
β-strand	1077-1082	6	17
α-helix	1084-1086	3
β-strand	1088-1095	8	18
β-strand	1100I-1103	4	18
β-strand	1107-1111	5	18
α-helix	1115-1116	2
β-strand	1117	1	19
α-helix	1118-1119	2
β-strand	1120-1124	5	20
α-helix	1125-1127	3
β-strand	1135-1145	11	20
β-strand	1146	1	19
β-strand	1151-1154	4	21
α-helix	1155-1157	3
β-strand	1159	1	21
β-strand	1163-1165	3	20
α-helix	1166-1168	3
β-strand	1169-1170	2	20
β-strand	1176-1185	10	20
α-helix	1186-1189	4
β-strand	1194-1200	7	21
α-helix	1201-1203	3
β-strand	1205-1211	7	21

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	-1-3	5
β-strand	4-7	4	22
β-strand	10-14	5	23
β-strand	19-25	7	22
β-strand	33-38	6	23
β-strand	45-49	5	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-67	6	22
β-strand	70-75	6	22
α-helix	80-82	3
β-strand	84-90	7	23
α-helix	96	1
β-strand	97-98	2	23
β-strand	102-107	6	23
β-strand	111	1	24
α-helix	112-113	2
β-strand	114-118	5	25
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	25
β-strand	140	1	24
β-strand	145-150	6	26
β-strand	153-154	2	26
α-helix	155	1
β-strand	159-163	5	25
α-helix	164-167	4
β-strand	173-182	10	25
α-helix	183-188	6
β-strand	191-198	8	26
β-strand	201-208	8	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A	protein	613	Homo sapiens	O75581 (AlphaFold model)
YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker	H	protein	276	Homo sapiens
YW210.09 Fab light chain	L	protein	225	Homo sapiens

Sequence of entity 1 (A), FASTA

>8FFE_1 Low-density lipoprotein receptor-related protein 6 (chains A)
APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTE
FNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQ
PRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKLYWA
DAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLR
EIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLEN
GKTCKDGATELLLLARRTDLRRISLDTPDFTDIVLQLEDIRHAIAIDYDPVEGYIYWTDD
EVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYWTDTGTDRIEVTRLNGTMRKI
LISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGWPNGLALDY
DEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQRRSIERVH
KRSAEREVIIDQLPDLMGLKATNVHRVIGSNPCAEENGGCSHLCLYRPQGLRCACPIGFE
LISDMKTCIVPEH

Sequence of entity 2 (H), FASTA

>8FFE_2 YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker (chains H)
DPCTNSVNCRRAIADAFSGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGF
TFTNSYIHWVRQAPGKGLEWVGWITPYGGYTNYADSVKGRFTISADTSKNTAYLQMNSLR
AEDTAVYYCARGSGHVNAVKNYGYVMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGG
TAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTY
ICNVNHKPSNTKVDKKVEPKSCDKTHSRGGLEVLFQ

Sequence of entity 3 (L), FASTA

>8FFE_3 YW210.09 Fab light chain (chains L)
ADPDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSG
VPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGECSRGGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
SIN	Succinic acid	C4 H6 O4	1

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

Primary citation

Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for coreceptor discrimination. Tsutsumi, N., Hwang, S., Waghray, D. et al. Proc Natl Acad Sci U S A (2023) 120:e2218238120-e2218238120. DOI 10.1073/pnas.2218238120 · 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
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
6H15 2.6 Å, Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10

Browse structure collections

About this viewer

MolViewer shows 8FFE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.