3S94: LRP6-E1E2

Crystal structure of LRP6-E1E2. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Nov 2011.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,406
Mol. weight: 141.35 kDa
Ligands: NAG
Released: 2 Nov 2011

Explore 3S94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S94 contains 13 α-helices and 114 β-strands across 2 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, 57 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	30	1	2
β-strand	31-34	4	1
β-strand	48	1	2
β-strand	53-59	7	3
β-strand	64-69	6	3
β-strand	74-79	6	3
β-strand	87-90	4	3
β-strand	97-103	7	4
β-strand	108-113	6	4
β-strand	118-123	6	4
β-strand	130-133	4	4
β-strand	143-146	4	5
β-strand	151-156	6	5
β-strand	162-167	6	5
β-strand	174-177	4	5
β-strand	184-190	7	6
β-strand	195-200	6	6
β-strand	206-209	4	6
β-strand	215-216	2	6
β-strand	230-232	3	7
β-strand	236-240	5	7
β-strand	247-251	5	7
β-strand	259-260	2	7
β-strand	270-273	4	1
α-helix	276-278	3
α-helix	290-292	3
β-strand	296-299	4	8
β-strand	306-309	4	8
α-helix	314-315	2
β-strand	316	1	9
α-helix	317	1
β-strand	323	1	9
β-strand	329-335	7	10
β-strand	339-343	5	10
β-strand	352-353	2	10
α-helix	354	1
β-strand	362-368	7	11
β-strand	373-378	6	11
β-strand	383-388	6	11
β-strand	395-398	4	11
β-strand	407-411	5	12
β-strand	416-421	6	12
β-strand	426-431	6	12
β-strand	438-441	4	12
β-strand	448-454	7	13
β-strand	459-464	6	13
β-strand	470-475	6	13
β-strand	482-485	4	13
β-strand	492-498	7	14
β-strand	503-508	6	14
β-strand	513-518	6	14
β-strand	525-529	5	14
β-strand	538-541	4	15
β-strand	544-548	5	15
β-strand	555-559	5	15
β-strand	565-569	5	15
β-strand	575-582	8	10
α-helix	591-593	3
α-helix	595-598	4
β-strand	602-606	5	16
β-strand	609-613	5	16
β-strand	619-620	2	17
β-strand	627-628	2	17

Chain B: 6 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	18
β-strand	30-33	4	18
β-strand	47-48	2	18
β-strand	53-59	7	19
β-strand	64-69	6	19
β-strand	74-78	5	19
β-strand	88-89	2	19
β-strand	99-103	5	20
β-strand	108-113	6	20
β-strand	118-123	6	20
β-strand	130-133	4	20
β-strand	140-146	7	21
β-strand	151-156	6	21
β-strand	162-167	6	21
β-strand	174-177	4	21
β-strand	184-190	7	22
β-strand	195-200	6	22
β-strand	206-209	4	22
β-strand	217-218	2	22
β-strand	232	1	23
β-strand	236-238	3	23
β-strand	247-248	2	24
β-strand	249-251	3	23
β-strand	260-262	3	24
β-strand	271-272	2	18
α-helix	276-278	3
β-strand	296-299	4	25
β-strand	306-309	4	25
α-helix	314-315	2
β-strand	316	1	26
α-helix	317	1
β-strand	323	1	26
β-strand	329-335	7	27
β-strand	339-343	5	27
β-strand	353	1	27
β-strand	362-368	7	28
β-strand	373-378	6	28
β-strand	384-387	4	28
β-strand	395-398	4	28
β-strand	405-411	7	29
β-strand	416-421	6	29
β-strand	426-431	6	29
β-strand	438-441	4	29
β-strand	448-454	7	30
β-strand	459-465	7	30
β-strand	469-475	7	30
β-strand	482-485	4	30
β-strand	492-498	7	31
β-strand	503-508	6	31
β-strand	513-518	6	31
β-strand	525-529	5	31
α-helix	532-533	2
β-strand	538-540	3	32
β-strand	544-548	5	32
α-helix	549	1
β-strand	555-559	5	32
β-strand	565-567	3	32
β-strand	575-582	8	27
α-helix	595-598	4
β-strand	602-604	3	33
β-strand	611-613	3	33
β-strand	619-620	2	34
β-strand	627-628	2	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A, B	protein	619	Homo sapiens	O75581 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3S94_1 Low-density lipoprotein receptor-related protein 6 (chains A, B)
HHHHHHHHAPLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVS
EEAIKRTEFNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKV
LFWQELDQPRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDY
EEQKLYWADAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACN
KYTGEGLREIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACP
TGVKLLENGKTCKDGATELLLLARRTDLRRISLDTPDFTDIVLQLEDIRHAIAIDYDPVE
GYIYWTDDEVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYWTDTGTDRIEVTR
LNGTMRKILISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGW
PNGLALDYDEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQ
RRSIERVHKRSAEREVIIDQLPDLMGLKATNVHRVIGSNPCAEENGGCSHLCLYRPQGLR
CACPIGFELISDMKTCIVP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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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