6NMJ

Crystal Structure of Rat Ric-8A G alpha binding domain, "Paratone-N Immersed"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


Literature

Structure, Function, and Dynamics of the G alpha Binding Domain of Ric-8A.

Zeng, B.Mou, T.C.Doukov, T.I.Steiner, A.Yu, W.Papasergi-Scott, M.Tall, G.G.Hagn, F.Sprang, S.R.

(2019) Structure 27: 1137-1147.e5

  • DOI: https://doi.org/10.1016/j.str.2019.04.013
  • Primary Citation of Related Structures:  
    6NMG, 6NMJ

  • PubMed Abstract: 

    Ric-8A is a 530-amino acid cytoplasmic molecular chaperone and guanine nucleotide exchange factor (GEF) for i, q, and 12/13 classes of heterortrimeric G protein alpha subunits (Gα). We report the 2.2-Å crystal structure of the Ric-8A Gα-binding domain with GEF activity, residues 1-452, and is phosphorylated at Ser435 and Thr440. Residues 1-429 adopt a superhelical fold comprised of Armadillo (ARM) and HEAT repeats, and the C terminus is disordered. One of the phosphorylated residues potentially binds to a basic cluster in an ARM motif. Amino acid sequence conservation and published hydrogen-deuterium exchange data indicate repeats 3 through 6 to be a putative Gα-binding surface. Normal mode modeling of small-angle X-ray scattering data indicates that phosphorylation induces relative rotation between repeats 1-4, 5-6, and 7-9. 2D 1 H- 15 N-TROSY spectra of [ 2 H, 15 N]-labeled Gαi1 in the presence of R452 reveals chemical shift perturbations of the C terminus and Gαi1 residues involved in nucleotide binding.


  • Organizational Affiliation

    Graduate Program in Biochemistry and Biophysics, University of Montana, Missoula, MT 59812, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
A, B
453Rattus norvegicusMutation(s): 1 
Gene Names: Ric8arCG_48458
UniProt
Find proteins for B1H241 (Rattus norvegicus)
Explore B1H241 
Go to UniProtKB:  B1H241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1H241
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.298α = 90
b = 100.114β = 90
c = 129.959γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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 States5R01GM105993
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103546

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description