3SJQ

Crystal structure of a small conductance potassium channel splice variant complexed with calcium-calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for calmodulin as a dynamic calcium sensor.

Zhang, M.Abrams, C.Wang, L.Gizzi, A.He, L.Lin, R.Chen, Y.Loll, P.J.Pascal, J.M.Zhang, J.F.

(2012) Structure 20: 911-923

  • DOI: https://doi.org/10.1016/j.str.2012.03.019
  • Primary Citation of Related Structures:  
    3SJQ

  • PubMed Abstract: 

    Calmodulin is a prototypical and versatile Ca(2+) sensor with EF hands as its high-affinity Ca(2+) binding domains. Calmodulin is present in all eukaryotic cells, mediating Ca(2+)-dependent signaling. Upon binding Ca(2+), calmodulin changes its conformation to form complexes with a diverse array of target proteins. Despite a wealth of knowledge on calmodulin, little is known on how target proteins regulate calmodulin's ability to bind Ca(2+). Here, we take advantage of two splice variants of SK2 channels, which are activated by Ca(2+)-bound calmodulin but show different sensitivity to Ca(2+) for their activation. Protein crystal structures and other experiments show that, depending on which SK2 splice variant it binds to, calmodulin adopts drastically different conformations with different affinities for Ca(2+) at its C-lobe. Such target protein-induced conformational changes make calmodulin a dynamic Ca(2+) sensor capable of responding to different Ca(2+) concentrations in cellular Ca(2+) signaling.


  • Organizational Affiliation

    Department of Molecular Physiology and Biophysics, Jefferson Medical College, Philadelphia, PA 19107, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin
A, B
149Rattus norvegicusMutation(s): 0 
Gene Names: Calm1CalmCamCam1Calm2Cam2CambCalm3Cam3Camc
UniProt
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP29
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small conductance calcium-activated potassium channel protein 2
C, D
87Rattus norvegicusMutation(s): 3 
Gene Names: Kcnn2
UniProt
Find proteins for P70604 (Rattus norvegicus)
Explore P70604 
Go to UniProtKB:  P70604
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70604
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHU
Query on PHU

Download Ideal Coordinates CCD File 
DA [auth D],
I [auth A],
T [auth B],
Z [auth C]
1-phenylurea
C7 H8 N2 O
LUBJCRLGQSPQNN-UHFFFAOYSA-N
SO4
Query on SO4

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BA [auth D]
CA [auth D]
N [auth A]
O [auth A]
V [auth B]
BA [auth D],
CA [auth D],
N [auth A],
O [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
AA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
P [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.74α = 90.68
b = 65.63β = 110.45
c = 66.08γ = 111.02
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description