6TYL

Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report



Literature

Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to G alpha i1.

McClelland, L.J.Zhang, K.Mou, T.C.Johnston, J.Yates-Hansen, C.Li, S.Thomas, C.J.Doukov, T.I.Triest, S.Wohlkonig, A.Tall, G.G.Steyaert, J.Chiu, W.Sprang, S.R.

(2020) Nat Commun 11: 1077-1077

  • DOI: 10.1038/s41467-020-14943-4
  • Primary Citation of Related Structures:  
    6TYL, 6UKT

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Graduate Program in Biochemistry and Biophysics, University of Montana, Missoula, MT, 59812, USA. Stephen.sprang@umontana.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)A, F492Rattus norvegicusMutation(s): 1 
Gene Names: Ric8arCG_48458
Find proteins for B1H241 (Rattus norvegicus)
Explore B1H241 
Go to UniProtKB:  B1H241
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody AC, H124Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody BE, J131Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody CD, I134Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B, G354Rattus norvegicusMutation(s): 0 
Gene Names: Gnai1Gnai-1
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,FL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,FL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.048α = 90
b = 144.726β = 94.66
c = 114.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP20GM103546
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM105993
National Science Foundation (United States)United States1738547

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release