3SOV: Beta propeller domain

The structure of a beta propeller domain in complex with peptide S. Determined by X-ray diffraction at 1.27 Å resolution. Released 21 Sept 2011.

Method: X-ray diffraction
Resolution: 1.27 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,050
Mol. weight: 37.83 kDa
Ligands: NAG, FUC
Released: 21 Sept 2011

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

Secondary structure: helices and β-sheets

3SOV contains 10 α-helices and 29 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: 9 helices, 29 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	88-92	5	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
α-helix	147-149	3
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	217-220	4	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	271-274	4	1
α-helix	276-278	3
α-helix	290-292	3
β-strand	296-299	4	7
β-strand	306-309	4	7
α-helix	314-315	2
β-strand	316	1	8
α-helix	317	1
α-helix	322	1
β-strand	323	1	8
α-helix	324	1

Chain Z: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A	protein	318	Homo sapiens	O75581 (AlphaFold model)
Sclerostin	Z	protein	9	Homo sapiens	Q9BQB4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3SOV_1 Low-density lipoprotein receptor-related protein 6 (chains A)
AGSAPLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIK
RTEFNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQE
LDQPRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKL
YWADAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGE
GLREIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKL
LENGKTCKDGNSHHHHHH

Sequence of entity 2 (Z), FASTA

>3SOV_2 Sclerostin (chains Z)
XLPNAIGRX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
FUC	alpha-L-fucopyranose	C6 H12 O5	4

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

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:

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
6H15 2.6 Å, Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10

Browse structure collections

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