Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 103.26 kDa 
• Atom Count: 6339 
• Modelled Residue Count: 796 
• Deposited Residue Count: 927 
• Unique protein chains: 2

6N85

Resistance to inhibitors of cholinesterase 8A (Ric8A) protein in complex with MBP-tagged transducin-alpha residues 327-350

• PDB DOI: 10.2210/pdb6N85/pdb

• Classification: CHAPERONE
• Organism(s): Bos taurus, Escherichia coli O157:H7, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-11-28 Released: 2019-07-10 
• Deposition Author(s): Srivastava, D., Gakhar, L., Artemyev, N.O.
• Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Structural underpinnings of Ric8A function as a G-protein alpha-subunit chaperone and guanine-nucleotide exchange factor.

Srivastava, D., Gakhar, L., Artemyev, N.O.

(2019) Nat Commun 10: 3084-3084

• PubMed: 31300652 
• DOI: 10.1038/s41467-019-11088-x
• Primary Citation of Related Structures:  
  6N84, 6N85, 6N86


• PubMed Abstract: 
  

Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level.

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Organizational Affiliation: 

Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synembryn-A	A [auth B]	512	Bos taurus	Mutation(s): 3  Gene Names: RIC8A
UniProt
Find proteins for Q5E9J8 (Bos taurus) Explore Q5E9J8  Go to UniProtKB:  Q5E9J8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Guanine nucleotide-binding protein G(t) subunit alpha-2	B [auth M]	415	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 7  Gene Names: malE, Z5632, ECs5017, GNAT2, GNATC
UniProt & NIH Common Fund Data Resources
Find proteins for P19087 (Homo sapiens) Explore P19087  Go to UniProtKB:  P19087
PHAROS:  P19087
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
UniProt Groups	P19087P0AEY0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C [auth A]	alpha-maltose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.74	α = 90
b = 91.92	β = 112.3
c = 86.23	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-28 
• Released Date: 2019-07-10 
Deposition Author(s): Srivastava, D., Gakhar, L., Artemyev, N.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	NIH R01 EY12682

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2021-11-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary