SMTL ID : 7rhq.1

Cryo-EM structure of Xenopus Patched-1 in complex with GAS1 and Sonic Hedgehog

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: Y.296, A.298, N.302 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: E.811, N.989, Y.990, L.993 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.82, P.88, E.91, L.112 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL(Non-covalent)(Covalent)

CLR.4: 7 residues within 4Å: Chain A: L.106, A.109, L.111, V.427, V.432, A.468, F.485 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.106, A:L.106, A:A.109, A:L.111, A:V.432, A:F.485 CLR.8: 12 residues within 4Å: Chain B: Y.57, G.191, G.192 Chain C: R.135, L.148, Y.151, M.175, L.184, N.185, E.193, K.201, M.204 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.57, C:L.148, C:L.184, C:N.185, C:E.193

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 15 residues within 4Å: Chain A: V.206, I.210, Y.214, P.215, W.246, L.258, L.263, H.264, I.265, W.268, I.272, V.277, L.320 Chain C: L.18, G.22 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.206, A:I.210, A:Y.214, A:Y.214, A:W.246, A:L.258, A:I.265, A:I.272, A:V.277, A:L.320, C:L.18, C:L.18 Hydrogen bonds: A:H.264

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain A: N.339, Q.343 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.865 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.865

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain B: H.129, H.135, D.142, H.175, H.177 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.129, B:H.135, B:D.142, B:D.142, B:H.177

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 3 residues within 4Å: Chain B: E.67, E.103, D.106 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.67, B:E.103, B:D.106 CA.11: 5 residues within 4Å: Chain B: E.66, E.67, D.72, T.102, E.103 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.66, B:E.67, B:D.72, B:D.72, B:T.102

1 x PLM: PALMITIC ACID(Covalent)

PLM.12: 11 residues within 4Å: Chain A: V.115, W.119, A.487, A.488, A.559, L.767, I.770, F.1006, W.1007, F.1136 Chain B: C.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.115, A:W.119, A:A.487, A:A.488, A:A.559, A:L.767, A:I.770, A:F.1006, A:W.1007, A:F.1136 Hydrogen bonds: A:Y.791

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, P. et al., Structural basis for catalyzed assembly of the Sonic hedgehog-Patched1 signaling complex. Dev.Cell (2022)

Release Date

2022-03-02

Peptides

Patched-1: A
Sonic hedgehog protein N-product: B
Growth arrest-specific protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
G

Membrane

We predict this structure to be a membrane protein.
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Patched-1

Sonic hedgehog protein N-product

Growth arrest-specific protein 1

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