3UZS

Structure of the C13.28 RNA Aptamer Bound to the G Protein-Coupled Receptor Kinase 2-Heterotrimeric G Protein Beta 1 and Gamma 2 Subunit Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.52 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer.

Tesmer, V.M.Lennarz, S.Mayer, G.Tesmer, J.J.

(2012) Structure 20: 1300-1309

  • DOI: 10.1016/j.str.2012.05.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cardiovascular homeostasis is maintained in part by the rapid desensitization of activated heptahelical receptors that have been phosphorylated by G protein-coupled receptor kinase 2 (GRK2). However, during chronic heart failure GRK2 is upregulated a ...

    Cardiovascular homeostasis is maintained in part by the rapid desensitization of activated heptahelical receptors that have been phosphorylated by G protein-coupled receptor kinase 2 (GRK2). However, during chronic heart failure GRK2 is upregulated and believed to contribute to disease progression. We have determined crystallographic structures of GRK2 bound to an RNA aptamer that potently and selectively inhibits kinase activity. Key to the mechanism of inhibition is the positioning of an adenine nucleotide into the ATP-binding pocket and interactions with the basic αF-αG loop region of the GRK2 kinase domain. Constraints imposed on the RNA by the terminal stem of the aptamer also play a role. These results highlight how a high-affinity aptamer can be used to selectively trap a novel conformational state of a protein kinase.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA. tesmerjj@umich.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-adrenergic receptor kinase 1
A
689Bos taurusMutation(s): 1 
Gene Names: GRK2 (ADRBK1)
EC: 2.7.11.15
Find proteins for P21146 (Bos taurus)
Go to Gene View: GRK2
Go to UniProtKB:  P21146
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
340Bos taurusMutation(s): 0 
Gene Names: GNB1
Find proteins for P62871 (Bos taurus)
Go to Gene View: GNB1
Go to UniProtKB:  P62871
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
74Bos taurusMutation(s): 0 
Gene Names: GNG2
Find proteins for P63212 (Bos taurus)
Go to Gene View: GNG2
Go to UniProtKB:  P63212
Entity ID: 4
MoleculeChainsLengthOrganism
C13.28 RNA AptamerC28N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMT
Query on CMT
G
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.52 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.184 
  • Space Group: P 3 1 2
Unit Cell:
Length (Å)Angle (°)
a = 257.277α = 90.00
b = 257.277β = 90.00
c = 99.429γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references