6O5G

Calmodulin in complex with isomalbrancheamide D

  • Classification: METAL BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2019-03-02 Released: 2019-08-07 
  • Deposition Author(s): Beyett, T.S., Fraley, A.E., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 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 U S A 116: 15895-15900

  • DOI: 10.1073/pnas.1818547116
  • Primary Citation of Related Structures:  
    6EEB, 6O5G

  • 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 of cardiac hypertrophy ...

    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

    Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1A152Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMJ (Subject of Investigation/LOI)
Query on LMJ

Download Ideal Coordinates CCD File 
B [auth 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
C21 H23 Br Cl N3 O
HGDDRCCRXJDDLU-DQLDELGASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LMJ Binding MOAD:  6O5G Kd: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.858α = 90
b = 56.754β = 90
c = 117.168γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL071818
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL122416
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA70375
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118101

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence