2M5E | pdb_00002m5e

Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel NaV1.2.

Hovey, L.Fowler, C.A.Mahling, R.Lin, Z.Miller, M.S.Marx, D.C.Yoder, J.B.Kim, E.H.Tefft, K.M.Waite, B.C.Feldkamp, M.D.Yu, L.Shea, M.A.

(2017) Biophys Chem 224: 1-19

  • DOI: https://doi.org/10.1016/j.bpc.2017.02.006
  • Primary Citation Related Structures: 
    2M5E

  • PubMed Abstract: 

    Several members of the voltage-gated sodium channel family are regulated by calmodulin (CaM) and ionic calcium. The neuronal voltage-gated sodium channel Na V 1.2 contains binding sites for both apo (calcium-depleted) and calcium-saturated CaM. We have determined equilibrium dissociation constants for rat Na V 1.2 IQ motif [IQRAYRRYLLK] binding to apo CaM (~3nM) and (Ca 2+ ) 4 -CaM (~85nM), showing that apo CaM binding is favored by 30-fold. For both apo and (Ca 2+ ) 4 -CaM, NMR demonstrated that Na V 1.2 IQ motif peptide (Na V 1.2 IQp ) exclusively made contacts with C-domain residues of CaM (CaM C ). To understand how calcium triggers conformational change at the CaM-IQ interface, we determined a solution structure (2M5E.pdb) of (Ca 2+ ) 2 -CaM C bound to Na V 1.2 IQp . The polarity of (Ca 2+ ) 2 -CaM C relative to the IQ motif was opposite to that seen in apo CaM C -Na v 1.2 IQp (2KXW), revealing that CaM C recognizes nested, anti-parallel sites in Na v 1.2 IQp . Reversal of CaM may require transient release from the IQ motif during calcium binding, and facilitate a re-orientation of CaM N allowing interactions with non-IQ Na V 1.2 residues or auxiliary regulatory proteins interacting in the vicinity of the IQ motif.


  • Organizational Affiliation
    • Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States.

Macromolecule Content 

  • Total Structure Weight: 11.87 kDa 
  • Atom Count: 821 
  • Modeled Residue Count: 100 
  • Deposited Residue Count: 100 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin73Paramecium tetraureliaMutation(s): 0 
Gene Names: CAMGSPATT00015825001
UniProt
Find proteins for P07463 (Paramecium tetraurelia)
Explore P07463 
Go to UniProtKB:  P07463
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07463
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 2 subunit alpha27Rattus norvegicusMutation(s): 0 
Gene Names: Scn2aScn2a1
UniProt
Find proteins for P04775 (Rattus norvegicus)
Explore P04775 
Go to UniProtKB:  P04775
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04775
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references