3AH8

Structure of heterotrimeric G protein Galpha-q beta gamma in complex with an inhibitor YM-254890


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 

Starting Models: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structural basis for the specific inhibition of heterotrimeric Gq protein by a small molecule.

Nishimura, A.Kitano, K.Takasaki, J.Taniguchi, M.Mizuno, N.Tago, K.Hakoshima, T.Itoh, H.

(2010) Proc Natl Acad Sci U S A 107: 13666-13671

  • DOI: https://doi.org/10.1073/pnas.1003553107
  • Primary Citation of Related Structures:  
    3AH8

  • PubMed Abstract: 

    Heterotrimeric GTP-binding proteins (G proteins) transmit extracellular stimuli perceived by G protein-coupled receptors (GPCRs) to intracellular signaling cascades. Hundreds of GPCRs exist in humans and are the targets of a large percentage of the pharmaceutical drugs used today. Because G proteins are regulated by GPCRs, small molecules that directly modulate G proteins have the potential to become therapeutic agents. However, strategies to develop modulators have been hampered by a lack of structural knowledge of targeting sites for specific modulator binding. Here we present the mechanism of action of the cyclic depsipeptide YM-254890, which is a recently discovered Gq-selective inhibitor. YM-254890 specifically inhibits the GDP/GTP exchange reaction of alpha subunit of Gq protein (Galphaq) by inhibiting the GDP release from Galphaq. X-ray crystal structure analysis of the Galphaqbetagamma-YM-254890 complex shows that YM-254890 binds the hydrophobic cleft between two interdomain linkers connecting the GTPase and helical domains of the Galphaq. The binding stabilizes an inactive GDP-bound form through direct interactions with switch I and impairs the linker flexibility. Our studies provide a novel targeting site for the development of small molecules that selectively inhibit each Galpha subunit and an insight into the molecular mechanism of G protein activation.


  • Organizational Affiliation

    Signal Transduction Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1/Guanine nucleotide-binding protein G(q) subunit alpha chimeric protein355Rattus norvegicusMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: gmhB
EC: 3.6.5
UniProt
Find proteins for P10824 (Rattus norvegicus)
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Go to UniProtKB:  P10824
Find proteins for P21279 (Mus musculus)
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Go to UniProtKB:  P21279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP21279P10824
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Bos taurusMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
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Go to UniProtKB:  P62871
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UniProt GroupP62871
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]78Bos taurusMutation(s): 1 
Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus)
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Go to UniProtKB:  P63212
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UniProt GroupP63212
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
YM-254890D [auth Y]9Chromobacterium sp.Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
HL2
Query on HL2
D [auth Y]L-PEPTIDE LINKINGC6 H13 N O3LEU
MAA
Query on MAA
D [auth Y]L-PEPTIDE LINKINGC4 H9 N O2ALA
OTH
Query on OTH
D [auth Y]L-PEPTIDE LINKINGC6 H13 N O3THR
THC
Query on THC
D [auth Y]L-PEPTIDE LINKINGC6 H11 N O4THR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.336α = 90
b = 173.336β = 90
c = 60.946γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2017-08-02
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations