1CIP | pdb_00001cip

GI-ALPHA-1 SUBUNIT OF GUANINE NUCLEOTIDE-BINDING PROTEIN COMPLEXED WITH A GTP ANALOGUE

• PDB DOI: https://doi.org/10.2210/pdb1CIP/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-05 Released: 1999-04-09 
• Deposition Author(s): Coleman, D., Sprang, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.201 (DCC) 

Starting Model: experimental

Literature

Structure of Gialpha1.GppNHp, autoinhibition in a galpha protein-substrate complex.

Coleman, D.E., Sprang, S.R.

(1999) J Biological Chem 274: 16669-16672

• PubMed: 10358003 
• DOI: https://doi.org/10.1074/jbc.274.24.16669
• Primary Citation Related Structures: 
  1CIP


• PubMed Abstract: 
  

  The structure of the G protein Gialpha1 complexed with the nonhydrolyzable GTP analog guanosine-5'-(betagamma-imino)triphosphate (GppNHp) has been determined at a resolution of 1.5 A. In the active site of Gialpha1. GppNHp, a water molecule is hydrogen bonded to the side chain of Glu43 and to an oxygen atom of the gamma-phosphate group. The side chain of the essential catalytic residue Gln204 assumes a conformation which is distinctly different from that observed in complexes with either guanosine 5'-O-3-thiotriphosphate or the transition state analog GDP.AlF4-. Hydrogen bonding and steric interactions position Gln204 such that it interacts with a presumptive nucleophilic water molecule, but cannot interact with the pentacoordinate transition state. Gln204 must be released from this auto-inhibited state to participate in catalysis. RGS proteins may accelerate the rate of GTP hydrolysis by G protein alpha subunits, in part, by inserting an amino acid side chain into the site occupied by Gln204, thereby destabilizing the auto-inhibited state of Galpha.

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Organizational Affiliation: 
• Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75235-9050, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.81 kDa 
• Atom Count: 2,733 
• Modeled Residue Count: 316 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-1 SUBUNIT)	A	353	Rattus norvegicus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P10824 (Rattus norvegicus) Explore P10824  Go to UniProtKB:  P10824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.235 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.201 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.05	α = 90
b = 80.05	β = 90
c = 105.55	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-09 
Deposition Author(s): Coleman, D., Sprang, S.

Revision History  

• Version 1.0: 1999-04-09
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description