3SOB: First YWTD beta propeller domain of LRP6

The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Sept 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,187
Mol. weight: 88.52 kDa
Ligands: CA
Released: 21 Sept 2011

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

Secondary structure: helices and β-sheets

3SOB contains 25 α-helices and 73 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 B: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	6
β-strand	28	1	7
β-strand	31-35	5	6
α-helix	36-38	3
α-helix	42-43	2
β-strand	44-47	4	6
β-strand	53-59	7	7
α-helix	60-62	3
β-strand	64-69	6	7
β-strand	74-79	6	7
β-strand	87-90	4	7
β-strand	99-103	5	8
β-strand	108-113	6	8
β-strand	118-123	6	8
β-strand	130-133	4	8
β-strand	140-146	7	9
α-helix	147-149	3
β-strand	151-156	6	9
β-strand	162-167	6	9
β-strand	174-177	4	9
β-strand	184-190	7	10
β-strand	195-200	6	10
β-strand	205-210	6	10
β-strand	217-220	4	10
β-strand	227-233	7	11
β-strand	236-241	6	11
β-strand	246-251	6	11
β-strand	259-262	4	11
β-strand	271-274	4	6
α-helix	276-278	3
α-helix	290-292	3
β-strand	296-299	4	12
β-strand	306-309	4	12
α-helix	314-315	2
β-strand	316	1	13
α-helix	317	1
β-strand	323	1	13

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	46-52	7	16
β-strand	56-59	4	16
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-95	8	16
β-strand	100I-103	4	16
β-strand	107-109	3	16
β-strand	110-111	2	15
α-helix	115-116	2
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
α-helix	155-157	3
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
α-helix	186-188	3
β-strand	195-200	6	19
α-helix	201-203	3
β-strand	205-210	6	19

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody light chain	L	protein	237	Homo sapiens
Low-density lipoprotein receptor-related protein 6	B	protein	316	Homo sapiens	O75581 (AlphaFold model)
antibody heavy chain	H	protein	256	Homo sapiens

Sequence of entity 1 (L), FASTA

>3SOB_1 antibody light chain (chains L)
MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQ
QKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPT
FGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>3SOB_2 Low-density lipoprotein receptor-related protein 6 (chains B)
APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTE
FNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQ
PRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKLYWA
DAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLR
EIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLEN
GKTCKDGATELLLLAR

Sequence of entity 3 (H), FASTA

>3SOB_3 antibody heavy chain (chains H)
MKKNIAFLLASMFVFSIATNAYAEVQLVESGGGLVQPGGSLRLSCAASGFTFTNSYIHWV
RQAPGKGLEWVGWITPYGGYTNYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCA
RGSGHVNAVKNYGYVMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKD
YFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSN
TKVDKKVEPKSCDKTH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Wnt antagonists bind through a short peptide to the first beta-propeller domain of LRP5/6. Bourhis, E., Wang, W., Tam, C. et al. Structure (2011) 19:1433-1442. DOI 10.1016/j.str.2011.07.005 · 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
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

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