1BOF | pdb_00001bof

GI-ALPHA-1 BOUND TO GDP AND MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.268 (Depositor), 0.381 (DCC) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Crystal structures of the G protein Gi alpha 1 complexed with GDP and Mg2+: a crystallographic titration experiment.

Coleman, D.E.Sprang, S.R.

(1998) Biochemistry 37: 14376-14385

  • DOI: https://doi.org/10.1021/bi9810306
  • Primary Citation Related Structures: 
    1BOF

  • PubMed Abstract: 

    The effect of Mg2+ binding on the conformation of the inactive GDP-bound complex of the heterotrimeric G protein alpha subunit Gi alpha 1 has been investigated by X-ray crystallography. Crystal structures of the Gi alpha 1.GDP complex were determined after titration with 5, 10, 100, and 200 mM Mg2+. Comparison of these structures with that of the Mg2+-free complex revealed Mg2+ bound at the same site as observed in the structure of the active, Gi alpha 1. GTP gamma S.Mg2+-bound complex of Gi alpha 1, with a similar coordination scheme except for the substitution of a water molecule for an oxygen ligand of the gamma-phosphate of Gi alpha 1.GTP gamma S. Mg2+. In contrast to the GDP.Mg2+ complex of Gt alpha and of other G proteins, switch I residues of Gi alpha 1 participate in Mg2+ binding and undergo conformational changes as a consequence of Mg2+ binding. Partial order is induced in switch II, which is disordered in the Mg2+-free complex, but no order is observed in the switch III region. This contrasts with the GDP.Mg2+ complex of Gt alpha in which both switch II and III switch are ordered. Mg2+ binding also induces binding of an SO42- molecule to the active site in a manner which may mimic a Gi alpha 1.GDP.PO42-.Mg2+ product complex. Implications of these findings are discussed.


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

Macromolecule Content 

  • Total Structure Weight: 40.93 kDa 
  • Atom Count: 2,677 
  • Modeled Residue Count: 324 
  • Deposited Residue Count: 353 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GI ALPHA 1353Rattus norvegicusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10824
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.268 (Depositor), 0.381 (DCC) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.747α = 90
b = 121.747β = 90
c = 68.929γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection