3NYN

Crystal Structure of G Protein-Coupled Receptor Kinase 6 in Complex with Sangivamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for activation of G protein-coupled receptor kinases.

Boguth, C.A.Singh, P.Huang, C.C.Tesmer, J.J.

(2010) Embo J. 29: 3249-3259

  • DOI: 10.1038/emboj.2010.206
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein-coupled receptor (GPCR) kinases (GRKs) selectively recognize and are allosterically regulated by activated GPCRs, but the molecular basis for this interaction is not understood. Herein, we report crystal structures of GRK6 in which regions ...

    G protein-coupled receptor (GPCR) kinases (GRKs) selectively recognize and are allosterically regulated by activated GPCRs, but the molecular basis for this interaction is not understood. Herein, we report crystal structures of GRK6 in which regions known to be critical for receptor phosphorylation have coalesced to stabilize the kinase domain in a closed state and to form a likely receptor docking site. The crux of this docking site is an extended N-terminal helix that bridges the large and small lobes of the kinase domain and lies adjacent to a basic surface of the protein proposed to bind anionic phospholipids. Mutation of exposed, hydrophobic residues in the N-terminal helix selectively inhibits receptor, but not peptide phosphorylation, suggesting that these residues interact directly with GPCRs. Our structural and biochemical results thus provide an explanation for how receptor recognition, phospholipid binding, and kinase activation are intimately coupled in GRKs.


    Organizational Affiliation

    Life Sciences Institute, The University of Michigan, Ann Arbor, MI, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G protein-coupled receptor kinase 6
A, B
576Homo sapiensMutation(s): 0 
Gene Names: GRK6 (GPRK6)
EC: 2.7.11.16
Find proteins for P43250 (Homo sapiens)
Go to Gene View: GRK6
Go to UniProtKB:  P43250
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, B
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
SGV
Query on SGV

Download SDF File 
Download CCD File 
A, B
SANGIVAMYCIN
4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide
C12 H15 N5 O5
OBZJZDHRXBKKTJ-JTFADIMSSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SGVKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.227 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 154.590α = 90.00
b = 154.590β = 90.00
c = 207.914γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance