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SMTL ID : 7y15.1

Cryo-EM structure of apo-state MrgD-Gi complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.1:	5 residues within 4Å: Chain D: L.250, F.254, I.256, W.257 Ligands: PLM.3 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.250, D:F.254, D:W.257, D:W.257 Hydrogen bonds: D:I.256, D:W.257
PLM.2:	6 residues within 4Å: Chain D: I.188, N.192, H.265, A.268, G.272, W.275 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.188 Salt bridges: D:H.265
PLM.3:	12 residues within 4Å: Chain D: Y.189, T.242, A.243, T.246, Q.247, L.250, R.262, L.266, V.270, L.274, L.277 Ligands: PLM.1 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:T.242, D:T.246, D:Q.247, D:L.250, D:V.270, D:L.274, D:L.277 Hydrogen bonds: D:Y.189, D:Q.247 Salt bridges: D:R.262

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Suzuki, S. et al., Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Commun Biol (2022)

Release Date

2022-07-20

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
Soluble cytochrome b562,Mas-related G-protein coupled receptor member D: 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

Soluble cytochrome b562,Mas-related G-protein coupled receptor member D

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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