SMTL ID : 8tzr.1

Structure of human Wnt3a bound to WLS and CALR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- GLC: alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-GLC.1: 20 residues within 4Å: Chain A: N.298, H.302 Chain B: K.168 Chain C: C.105, G.106, G.107, Y.109, K.111, G.124, Y.128, M.131, D.135, C.137, G.138, P.139, I.147, D.317, L.318, W.319, V.321 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.319, C:Y.128, C:Y.128, C:N.154, C:K.111

1 x PAM: PALMITOLEIC ACID(Covalent)

PAM.2: 9 residues within 4Å: Chain A: L.208, S.209 Chain B: D.301, G.305, S.346, F.347, L.349, F.350, D.353 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.347, B:L.349, B:F.350, B:F.350, B:D.353

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.3: 17 residues within 4Å: Chain A: E.213, V.214 Chain B: Q.226, F.230, W.234, K.238, I.280, Q.304, F.307, Y.308, T.446, F.450, F.473, F.474, I.477, Y.478, W.481 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.307, B:Y.308, B:F.450, B:F.473, B:F.474, B:W.481, B:W.481 Hydrogen bonds: B:W.234 Salt bridges: B:K.238 pi-Cation interactions: B:F.474

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qi, X. et al., Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling. Cell (2023)

Release Date

2023-10-18

Peptides

Protein Wnt-3a: A
Protein wntless homolog: B
Calreticulin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Protein Wnt-3a

Protein wntless homolog

Calreticulin

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