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), 0.245 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 160.34 kDa 
  • Atom Count: 10,424 
  • Modeled Residue Count: 1,256 
  • Deposited Residue Count: 1,380 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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 

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), 0.245 (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

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Ligand Structure Quality Assessment 


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