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SMTL ID : 7ew3.1

Cryo-EM structure of S1P-bound Sphingosine 1-phosphate receptor 3 in complex with Gi protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x S1P: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

S1P.1:

15 residues within 4Å:

Chain D: Y.56, K.61, R.65, N.129, S.133, T.137, R.148, E.149, M.152, F.153, L.156, L.202, I.237, F.294, I.318

12 PLIP interactions:

12 interactions with chain D

Hydrophobic interactions: D:F.153, D:L.156, D:L.156, D:L.202, D:I.237, D:F.294
Hydrogen bonds: D:Y.56, D:S.133, D:T.137, D:R.148
Salt bridges: D:K.61, D:R.65

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.2:	3 residues within 4Å: Chain D: I.281, V.285, A.335 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.281, D:V.285 Hydrogen bonds: D:A.335
PLM.3:	6 residues within 4Å: Chain D: I.168, H.171, L.172, T.244 Ligands: PLM.4, PLM.5 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.168, D:T.244 Hydrogen bonds: D:H.171
PLM.4:	8 residues within 4Å: Chain D: H.171, I.175, V.243, T.244, I.247, L.248, R.251 Ligands: PLM.3 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.243, D:I.247, D:L.248 Salt bridges: D:R.251
PLM.5:	5 residues within 4Å: Chain D: L.172, K.176, K.184, L.191 Ligands: PLM.3 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.191 Salt bridges: D:K.176, D:K.184

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Zhao, C. et al., Structural insights into sphingosine-1-phosphate recognition and ligand selectivity of S1PR3-Gi signaling complexes. Cell Res. (2022)

Release Date

2021-09-29

Peptides

Guanine nucleotide-binding protein G(i) subunit alpha-1: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: C
Sphingosine 1-phosphate receptor 3: D
scFV16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
R

E
S

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

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

Sphingosine 1-phosphate receptor 3

scFV16

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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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