6TYL image
Entry Detail
PDB ID:
6TYL
Title:
Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2019-08-09
Release Date:
2020-03-11
Method Details:
Experimental Method:
Resolution:
3.30 Å
R-Value Free:
0.28
R-Value Work:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
Mutations:Y232F
Chain IDs:A, J (auth: F)
Chain Length:492
Number of Molecules:2
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein G(i) subunit alpha-1
Chain IDs:H (auth: B), I (auth: G)
Chain Length:354
Number of Molecules:2
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Nanobody A
Chain IDs:B (auth: C), C (auth: H)
Chain Length:124
Number of Molecules:2
Biological Source:Lama glama
Polymer Type:polypeptide(L)
Description:Nanobody C
Chain IDs:F (auth: D), G (auth: I)
Chain Length:134
Number of Molecules:2
Biological Source:Lama glama
Polymer Type:polypeptide(L)
Description:Nanobody B
Chain IDs:D (auth: E), E (auth: J)
Chain Length:131
Number of Molecules:2
Biological Source:Lama glama
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER modified residue
TPO A THR modified residue
Ligand Molecules
Primary Citation
Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to G alpha i1.
Nat Commun 11 1077 1077 (2020)
PMID: 32103024 DOI: 10.1038/s41467-020-14943-4

Abstact

Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Gα bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Gα at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Gα binding sites. The C-terminus of Gα is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Gα beta sheet and switch II to stabilize the nucleotide-free state of Gα.

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Primary Citation of related structures