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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 pharm ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1/Guanine nucleotide-binding protein G(q) subunit alpha chimeric protein A355Rattus norvegicus, Mus musculus
This entity is chimeric		Mutation(s): 0 
Gene Names: gmhB
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 B340Bos taurusMutation(s): 0 
Gene Names: GNB1
Find proteins for P62871 (Bos taurus)
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Go to UniProtKB:  P62871
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 G78Bos taurusMutation(s): 1 
Gene Names: GNG2
Find proteins for P63212 (Bos taurus)
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Go to UniProtKB:  P63212
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
YM-254890 Y9Chromobacterium sp.Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
HL2
Query on HL2		YL-PEPTIDE LINKINGC6 H13 N O3LEU
MAA
Query on MAA		YL-PEPTIDE LINKINGC4 H9 N O2ALA
OTH
Query on OTH		YL-PEPTIDE LINKINGC6 H13 N O3THR
THC
Query on THC		YL-PEPTIDE LINKINGC6 H11 N O4THR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000482
Query on PRD_000482		YYM-254890Cyclic depsipeptide /  Inhibitor

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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

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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