6O5G

Calmodulin in complex with isomalbrancheamide D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe.

Beyett, T.S.Fraley, A.E.Labudde, E.Patra, D.Coleman, R.C.Eguchi, A.Glukhova, A.Chen, Q.Williams, R.M.Koch, W.J.Sherman, D.H.Tesmer, J.J.G.

(2019) Proc.Natl.Acad.Sci.USA 116: 15895-15900

  • DOI: 10.1073/pnas.1818547116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein-coupled receptor (GPCR) kinases (GRKs) are responsible for initiating desensitization of activated GPCRs. GRK5 is potently inhibited by the calcium-sensing protein calmodulin (CaM), which leads to nuclear translocation of GRK5 and promotion ...

    G protein-coupled receptor (GPCR) kinases (GRKs) are responsible for initiating desensitization of activated GPCRs. GRK5 is potently inhibited by the calcium-sensing protein calmodulin (CaM), which leads to nuclear translocation of GRK5 and promotion of cardiac hypertrophy. Herein, we report the architecture of the Ca 2+ ·CaM-GRK5 complex determined by small-angle X-ray scattering and negative-stain electron microscopy. Ca 2+ ·CaM binds primarily to the small lobe of the kinase domain of GRK5 near elements critical for receptor interaction and membrane association, thereby inhibiting receptor phosphorylation while activating the kinase for phosphorylation of soluble substrates. To define the role of each lobe of Ca 2+ ·CaM, we utilized the natural product malbrancheamide as a chemical probe to show that the C-terminal lobe of Ca 2+ ·CaM regulates membrane binding while the N-terminal lobe regulates receptor phosphorylation and kinase domain activation. In cells, malbrancheamide attenuated GRK5 nuclear translocation and effectively blocked the hypertrophic response, demonstrating the utility of this natural product and its derivatives in probing Ca 2+ ·CaM-dependent hypertrophy.


    Organizational Affiliation

    Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109.,Department of Chemistry, College of Natural Sciences, Colorado State University, Fort Collins, CO 80523.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.,Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140.,Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907; jtesmer@purdue.edu.,Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-1
A
152Homo sapiensMutation(s): 0 
Gene Names: CALM1 (CALM, CAM, CAM1)
Find proteins for P0DP23 (Homo sapiens)
Go to Gene View: CALM1
Go to UniProtKB:  P0DP23
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LMJ
Query on LMJ

Download SDF File 
Download CCD File 
A
(5aS,12aS,13aS)-9-bromo-8-chloro-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one
isomalbrancheamide D
C21 H23 Br Cl N3 O
HGDDRCCRXJDDLU-DQLDELGASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.858α = 90.00
b = 56.754β = 90.00
c = 117.168γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL071818
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL122416
National Institutes of Health/National Cancer InstituteUnited StatesCA70375
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118101

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references