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 6BUT | pdb_00006but

Solution structure of full-length apo mammalian calmodulin bound to the IQ motif of the human voltage-gated sodium channel NaV1.2

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-12-11 Released: 2019-06-19 
  • Deposition Author(s): Mahling, R., Kilpatrick, A.M., Shea, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6BUT

This is version 1.3 of the entry. See complete history. 

Literature

Na V 1.2 EFL domain allosterically enhances Ca 2+ binding to sites I and II of WT and pathogenic calmodulin mutants bound to the channel CTD.

Mahling, R., Hovey, L., Isbell, H.M., Marx, D.C., Miller, M.S., Kilpatrick, A.M., Weaver, L.D., Yoder, J.B., Kim, E.H., Andresen, C.N.J., Li, S., Shea, M.A.

(2021) Structure 

  • DOI: https://doi.org/10.1016/j.str.2021.03.002
  • Primary Citation Related Structures: 
    6BUT

  • PubMed Abstract: 

    Neuronal voltage-gated sodium channel Na V 1.2 C-terminal domain (CTD) binds calmodulin (CaM) constitutively at its IQ motif. A solution structure (6BUT) and other NMR evidence showed that the CaM N domain (CaM N ) is structurally independent of the C-domain (CaM C ) whether CaM is bound to the Na V 1.2 IQp (1,901-1,927) or Na V 1.2 CTD (1,777-1,937) with or without calcium. However, in the CaM + Na V 1.2 CTD complex, the Ca 2+ affinity of CaM N was more favorable than in free CaM, while Ca 2+ affinity for CaM C was weaker than in the CaM + Na V 1.2 IQp complex. The CTD EF-like (EFL) domain allosterically widened the energetic gap between CaM domains. Cardiomyopathy-associated CaM mutants (N53I(N54I), D95V(D96V), A102V(A103V), E104A(E105A), D129G(D130G), and F141L(F142L)) all bound the Na V 1.2 IQ motif favorably under resting (apo) conditions and bound calcium normally at CaM N sites. However, only N53I and A102V bound calcium at CaM C sites at [Ca 2+ ] < 100 μM. Thus, they are expected to respond like wild-type CaM to Ca 2+ spikes in excitable cells.


  • Organizational Affiliation: 
    • Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.

Macromolecule Content 

  • Total Structure Weight: 20.4 kDa 
  • Atom Count: 1,425 
  • Modeled Residue Count: 179 
  • Deposited Residue Count: 179 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-1148Homo sapiensMutation(s): 0 
Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 2 subunit alpha31Homo sapiensMutation(s): 0 
Gene Names: SCN2A, NAC2, SCN2A1, SCN2A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99250 (Homo sapiens)
Explore Q99250 
Go to UniProtKB:  Q99250
PHAROS:  Q99250
GTEx:  ENSG00000136531 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99250
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM57001
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesT32 NS045549

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2021-04-21
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references