5HIT | pdb_00005hit

Crystal Structure Analysis of Ca2+-calmodulin and a C-terminal EAG1 channel fragment

• PDB DOI: https://doi.org/10.2210/pdb5HIT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Gallus gallus, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-12 Released: 2016-09-14 
• Deposition Author(s): Marques-Carvalho, M.J., Morais-Cabral, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.268 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Models: experimental

Literature

Molecular Insights into the Mechanism of Calmodulin Inhibition of the EAG1 Potassium Channel.

Marques-Carvalho, M.J., Oppermann, J., Munoz, E., Fernandes, A.S., Gabant, G., Cadene, M., Heinemann, S.H., Schonherr, R., Morais-Cabral, J.H.

(2016) Structure 24: 1742-1754

• PubMed: 27618660 
• DOI: https://doi.org/10.1016/j.str.2016.07.020
• Primary Citation Related Structures: 
  5HIT


• PubMed Abstract: 
  

  The human EAG1 potassium channel belongs to the superfamily of KCNH voltage-gated potassium channels that have roles in cardiac repolarization and neuronal excitability. EAG1 is strongly inhibited by Ca ²⁺ /calmodulin (CaM) through a mechanism that is not understood. We determined the binding properties of CaM with each one of three previously identified binding sites (BDN, BDC1, and BDC2), analyzed binding to protein stretches that include more than one site, and determined the effect of neighboring globular domains on the binding properties. The determination of the crystal structure of CaM bound to BDC2 shows the channel fragment interacting with only the C lobe of calmodulin and adopting an unusual bent conformation. Based on this structure and on a functional and biochemical analysis of mutants, we propose a model for the mechanism of inhibition whereby the local conformational change induced by CaM binding at BDC2 lies at the basis of channel modulation.

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Organizational Affiliation: 
• Instituto de Biologia Molecular e Celular, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
Department of Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany.
Software 4 Science Developments, 15782 Santiago de Compostela, Spain.
Centre de Biophysique Moléculaire, CNRS UPR430, 45071 Orléans, France.
Instituto de Biologia Molecular e Celular, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.7 kDa 
• Atom Count: 1,257 
• Modeled Residue Count: 161 
• Deposited Residue Count: 164 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	A	147	Gallus gallus	Mutation(s): 0  Gene Names: CALM, CAM, RCJMB04_24e7
UniProt
Find proteins for P62149 (Gallus gallus) Explore P62149  Go to UniProtKB:  P62149

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium voltage-gated channel subfamily H member 1	B	17	Mus musculus	Mutation(s): 0  Gene Names: Kcnh1
UniProt
Find proteins for Q60603 (Mus musculus) Explore Q60603  Go to UniProtKB:  Q60603

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.268 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.624	α = 90
b = 121.137	β = 90
c = 73.855	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Marques-Carvalho, M.J., Morais-Cabral, J.H.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2016-09-28
  Changes: Database references
• Version 1.3: 2016-10-19
  Changes: Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description