3QC9 | pdb_00003qc9

Crystal structure of cross-linked bovine GRK1 T8C/N480C double mutant complexed with ADP and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Activation of G Protein-Coupled Receptor Kinase 1 Involves Interactions between Its N-Terminal Region and Its Kinase Domain.

Huang, C.C.Orban, T.Jastrzebska, B.Palczewski, K.Tesmer, J.J.

(2011) Biochemistry 50: 1940-1949

  • DOI: https://doi.org/10.1021/bi101606e
  • Primary Citation Related Structures: 
    3QC9

  • PubMed Abstract: 

    G protein-coupled receptor kinases (GRKs) phosphorylate activated G protein-coupled receptors (GPCRs) to initiate receptor desensitization. In addition to the canonical phosphoacceptor site of the kinase domain, activated receptors bind to a distinct docking site that confers higher affinity and activates GRKs allosterically. Recent mutagenesis and structural studies support a model in which receptor docking activates a GRK by stabilizing the interaction of its ∼20-amino acid N-terminal region with the kinase domain. This interaction in turn stabilizes a closed, more active conformation of the enzyme. To investigate the importance of this interaction for the process of GRK activation, we first validated the functionality of the N-terminal region in rhodopsin kinase (GRK1) by site-directed mutagenesis and then introduced a disulfide bond to cross-link the N-terminal region of GRK1 with its specific binding site on the kinase domain. Characterization of the kinetic and biophysical properties of the cross-linked protein showed that disulfide bond formation greatly enhances the catalytic efficiency of the peptide phosphorylation, but receptor-dependent phosphorylation, Meta II stabilization, and inhibition of transducin activation were unaffected. These data indicate that the interaction of the N-terminal region with the kinase domain is important for GRK activation but does not dictate the affinity of GRKs for activated receptors.


  • Organizational Affiliation
    • Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, United States.

Macromolecule Content 

  • Total Structure Weight: 247.77 kDa 
  • Atom Count: 15,806 
  • Modeled Residue Count: 1,935 
  • Deposited Residue Count: 2,172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhodopsin kinase
A, B, C, D
543Bos taurusMutation(s): 2 
Gene Names: GRK1RHOK
EC: 2.7.11.14
UniProt
Find proteins for P28327 (Bos taurus)
Explore P28327 
Go to UniProtKB:  P28327
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28327
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C],
P [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.696α = 88.07
b = 89.965β = 90.26
c = 122.638γ = 68.78
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
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: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description