6NMJ | pdb_00006nmj

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

• PDB DOI: https://doi.org/10.2210/pdb6NMJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-11 Released: 2019-06-26 
• Deposition Author(s): Zeng, B., Mou, T.C., Sprang, S.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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

• PubMed: 31155309 
• DOI: https://doi.org/10.1016/j.str.2019.04.013
• Primary Citation 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.

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Organizational Affiliation: 
• Graduate Program in Biochemistry and Biophysics, University of Montana, Missoula, MT 59812, USA.
Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
Macromolecular Crystallography Group, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94309, USA.
Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA.
Graduate Program in Biochemistry and Biophysics, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.32 kDa 
• Atom Count: 6,541 
• Modeled Residue Count: 813 
• Deposited Residue Count: 906 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)	A, B	453	Rattus norvegicus	Mutation(s): 1  Gene Names: Ric8a, rCG_48458
UniProt
Find proteins for Q80ZG1 (Rattus norvegicus) Explore Q80ZG1  Go to UniProtKB:  Q80ZG1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.298	α = 90
b = 100.114	β = 90
c = 129.959	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Zeng, B., Mou, T.C., Sprang, S.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM105993
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546

Revision History  

• 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