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


This is version 1.2 of the entry. See complete history


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: https://doi.org/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 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

    Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)A,
J [auth F]
492Rattus norvegicusMutation(s): 1 
Gene Names: Ric8arCG_48458
UniProt
Find proteins for B1H241 (Rattus norvegicus)
Explore B1H241 
Go to UniProtKB:  B1H241
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1H241
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody AB [auth C],
C [auth H]
124Lama glamaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody BD [auth E],
E [auth J]
131Lama glamaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody CF [auth D],
G [auth I]
134Lama glamaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1H [auth B],
I [auth G]
354Rattus norvegicusMutation(s): 0 
Gene Names: Gnai1Gnai-1
UniProt
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
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UniProt GroupP10824
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A,
J [auth F]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,
J [auth F]
L-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 Sciences (NIH/NIGMS)United StatesP20GM103546
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM105993
National Science Foundation (United States)United States1738547

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description