6N84 | pdb_00006n84

MBP-fusion protein of transducin-alpha residues 327-350

• PDB DOI: https://doi.org/10.2210/pdb6N84/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: 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: 1.75 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/s41467-019-11088-x
• Primary Citation 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 Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
Protein Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].
Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.56 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 392 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Guanine nucleotide-binding protein G(t) subunit alpha-2	A	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 P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P19087 (Homo sapiens) Explore P19087  Go to UniProtKB:  P19087
PHAROS:  P19087
UniProt Groups	P0AEX9P19087

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.07	α = 90
b = 83.07	β = 90
c = 109.229	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• 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 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.0: 2024-01-10
  Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary