9CKQ | pdb_00009ckq

Human G protein-coupled receptor kinase 5-D311N ligand-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into the catalytic cycle of G protein-coupled receptor kinase 5 and a possible regulatory site for potassium ion.

Chen, Y.Tesmer, J.J.G.

(2025) J Biological Chem 301: 110309-110309

  • DOI: https://doi.org/10.1016/j.jbc.2025.110309
  • Primary Citation Related Structures: 
    9CKO, 9CKP, 9CKQ, 9CKR, 9CKS, 9MX2

  • PubMed Abstract: 

    G protein-coupled receptor (GPCR) kinases (GRKs) instigateGPCR desensitization, but despite many available structures, a molecular understanding of their function and catalytic cycle remains incomplete. We present six GRK5 crystal structures that capture both open and closed states of its kinase domain as well as complexes with the ligands sangivamycin (Sgv), an adenosine analog, and ATP. The Sgv-bound structure is distinct from the previously reported GRK5·Sgv structure and features an ordered N-terminal helix that docks to the kinase hinge, mimicking its interactions in GPCR or Ca 2+ ·calmodulin-bound GRK complexes. GRK5 undergoes a dramatic conformational change in the crystals to a ligand-free, open state with a disordered N terminus when K + is omitted from the harvesting solution. This transition to a ligand-free structure, not structurally observed for the GRK4 subfamily, most likely occurs through the release of the K + ion from its binding site close to the kinase domain hinge in the Sgv-bound complex. Two structures of GRK5 in complex with Mg 2+ and Mn 2+ ·ATP were obtained via soaking crystals of the open state, which we hypothesize are reflective of a substrate-loading stage. Although K + significantly stabilizes GRK5 in its closed, near-active conformation, potassium citrate and KCl inhibit kinase activity just as potently as sodium citrate and NaCl, respectively, suggesting that K + traps a closed conformation compatible with Sgv-AMP but incompatible with ATP, thereby inhibiting the catalytic cycle. Thus, changes in K + concentration could play a regulatory role for GRK5 in scenarios where activated GPCRs are coupled to G protein-responsive potassium channels.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA.

Macromolecule Content 

  • Total Structure Weight: 68.8 kDa 
  • Atom Count: 4,040 
  • Modeled Residue Count: 490 
  • Deposited Residue Count: 597 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G protein-coupled receptor kinase 5597Homo sapiensMutation(s): 1 
Gene Names: GRK5GPRK5
EC: 2.7.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for P34947 (Homo sapiens)
Explore P34947 
Go to UniProtKB:  P34947
PHAROS:  P34947
GTEx:  ENSG00000198873 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34947
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.272α = 90
b = 137.272β = 90
c = 70.988γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL071818

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Database references