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SMTL ID : 6vn7.1

Cryo-EM structure of an activated VIP1 receptor-G protein complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.1:	7 residues within 4Å: Chain A: Y.211, L.247, G.251, S.254, M.258 Ligands: CLR.4, CLR.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.211, A:L.247
CLR.2:	5 residues within 4Å: Chain A: I.342, M.343, F.347, P.348, F.351 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.347, A:P.348, A:F.351
CLR.3:	4 residues within 4Å: Chain A: I.300, I.303, R.304, L.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.300, A:I.303, A:R.304, A:L.307
CLR.4:	5 residues within 4Å: Chain A: V.200, A.204, I.265 Ligands: CLR.1, PLM.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.200, A:I.265
CLR.5:	5 residues within 4Å: Chain A: F.256, S.279, W.282, I.283, T.290 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.282, A:W.282, A:I.283, A:T.290
CLR.6:	7 residues within 4Å: Chain A: H.167, I.170, L.174, F.208, W.250 Ligands: CLR.1, PLM.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.170, A:L.174, A:F.208, A:W.250

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.7:	4 residues within 4Å: Chain A: S.199, G.201 Ligands: CLR.4, CLR.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.199
PLM.8:	1 residues within 4Å: Chain A: L.331 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.331
PLM.9:	5 residues within 4Å: Chain A: T.131, I.135, G.138, L.139 Ligands: PLM.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.131, A:I.135
PLM.10:	5 residues within 4Å: Chain A: T.134, L.141, A.142, F.180 Ligands: PLM.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.134, A:L.141, A:A.142, A:F.180

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Duan, J. et al., Cryo-EM structure of an activated VIP1 receptor-G protein complex revealed by a NanoBiT tethering strategy. Nat Commun (2020)

Release Date

2020-09-02

Peptides

Vasoactive intestinal polypeptide receptor 1: A
Pituitary adenylate cyclase-activating polypeptide: B
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: C
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: D
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: E
Nanobody 35: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
L

C
A

D
B

E
G

F
N

Membrane

We predict this structure to be a membrane protein.
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Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Vasoactive intestinal polypeptide receptor 1

Pituitary adenylate cyclase-activating polypeptide

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Nanobody 35

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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