1Y3A | pdb_00001y3a

Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.280 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange

Johnston, C.A.Willard, F.S.Jezyk, M.R.Fredericks, Z.Bodor, E.T.Jones, M.B.Blaesius, R.Watts, V.J.Harden, T.K.Sondek, J.Ramer, J.K.Siderovski, D.P.

(2005) Structure 7: 1069-1080

  • DOI: https://doi.org/10.1016/j.str.2005.04.007
  • Primary Citation of Related Structures:  
    1Y3A

  • PubMed Abstract: 

    Heterotrimeric G proteins are molecular switches that regulate numerous signaling pathways involved in cellular physiology. This characteristic is achieved by the adoption of two principal states: an inactive, GDP bound state and an active, GTP bound state. Under basal conditions, G proteins exist in the inactive, GDP bound state; thus, nucleotide exchange is crucial to the onset of signaling. Despite our understanding of G protein signaling pathways, the mechanism of nucleotide exchange remains elusive. We employed phage display technology to identify nucleotide state-dependent Galpha binding peptides. Herein, we report a GDP-selective Galpha binding peptide, KB-752, that enhances spontaneous nucleotide exchange of Galpha(i) subunits. Structural determination of the Galpha(i1)/peptide complex reveals unique changes in the Galpha switch regions predicted to enhance nucleotide exchange by creating a GDP dissociation route. Our results cast light onto a potential mechanism by which Galpha subunits adopt a conformation suitable for nucleotide exchange.


  • Organizational Affiliation

    Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i), alpha-1 subunit
A, B, C, D
329Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KB752 peptide
E, F, G, H
16Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.280 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.943α = 90
b = 112.785β = 93.75
c = 109.49γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-27
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description