SMTL ID : 8fcz.1

Crystal structure of ground-state rhodopsin in complex with a nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-NAG-MAN.1: 10 residues within 4Å: Chain A: T.4, N.15, G.18, V.20 Chain C: Q.39, G.42, K.43, G.44, L.45, T.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.39, C:L.45, C:K.43

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

NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: M.1, N.2, S.281, D.282 Chain C: R.52, D.56, N.57 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.3: 12 residues within 4Å: Chain B: F.9, N.15, G.18, V.20, R.21, S.22 Chain D: Q.39, G.42, K.43, G.44, L.45, T.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.39, D:L.45, D:L.45

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

NAG-NAG.4: 8 residues within 4Å: Chain B: M.1, N.2, G.280, S.281, D.282 Chain D: R.52, D.56, N.57 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.56, D:D.56

2 x RET: RETINAL(Covalent)

RET.5: 18 residues within 4Å: Chain A: E.113, A.117, T.118, G.121, E.122, S.186, C.187, I.189, Y.191, M.207, F.208, F.212, F.261, W.265, Y.268, A.269, A.292, K.296 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.117, A:T.118, A:I.189, A:F.208, A:F.261, A:W.265, A:W.265, A:Y.268, A:K.296 RET.6: 18 residues within 4Å: Chain B: E.113, G.114, A.117, T.118, G.121, E.122, S.186, C.187, G.188, I.189, Y.191, M.207, F.212, W.265, Y.268, A.269, A.292, K.296 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.117, B:T.118, B:I.189, B:F.212, B:F.212, B:W.265, B:W.265, B:Y.268, B:Y.268, B:A.269, B:K.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, A. et al., Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Nat Commun (2023)

Release Date

2023-08-30

Peptides

Rhodopsin: AB
Nanobody Nb2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

Nanobody Nb2

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