Crystal structure of the amino-terminal domain of human cardiac troponin C in complex with cadmium at 1.4 resolution.

Experimental Data Snapshot

  • Resolution: 1.37 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

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The structure of cardiac troponin C regulatory domain with bound Cd(2+) reveals a closed conformation and unique ion coordination.

Zhang, X.L.Tibbits, G.F.Paetzel, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 722-734

  • DOI: https://doi.org/10.1107/S0907444913001182
  • Primary Citation of Related Structures:  
    3SD6, 3SWB, 4GJE, 4GJF, 4GJG

  • PubMed Abstract: 

    The amino-terminal domain of cardiac troponin C (cNTnC) is an essential Ca(2+) sensor found in cardiomyocytes. It undergoes a conformational change upon Ca(2+) binding and transduces the signal to the rest of the troponin complex to initiate cardiac muscle contraction. Two classical EF-hand motifs (EF1 and EF2) are present in cNTnC. Under physiological conditions, only EF2 binds Ca(2+); EF1 is a vestigial site that has lost its function in binding Ca(2+) owing to amino-acid sequence changes during evolution. Proteins with EF-hand motifs are capable of binding divalent cations other than calcium. Here, the crystal structure of wild-type (WT) human cNTnC in complex with Cd(2+) is presented. The structure of Cd(2+)-bound cNTnC with the disease-related mutation L29Q, as well as a structure with the residue differences D2N, V28I, L29Q and G30D (NIQD), which have been shown to have functional importance in Ca(2+) sensing at lower temperatures in ectothermic species, have also been determined. The structures resemble the overall conformation of NMR structures of Ca(2+)-bound cNTnC, but differ significantly from a previous crystal structure of Cd(2+)-bound cNTnC in complex with deoxycholic acid. The subtle structural changes observed in the region near the mutations may play a role in the increased Ca(2+) affinity. The 1.4 Å resolution WT cNTnC structure, which is the highest resolution structure yet obtained for cardiac troponin C, reveals a Cd(2+) ion coordinated in the canonical pentagonal bipyramidal geometry in EF2 despite three residues in the loop being disordered. A Cd(2+) ion found in the vestigial ion-binding site of EF1 is coordinated in a noncanonical `distorted' octahedral geometry. A comparison of the ion coordination observed within EF-hand-containing proteins for which structures have been solved in the presence of Cd(2+) is presented. A refolded WT cNTnC structure is also presented.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Troponin C, slow skeletal and cardiac muscles89Homo sapiensMutation(s): 0 
Gene Names: TNNCTNNC1
UniProt & NIH Common Fund Data Resources
Find proteins for P63316 (Homo sapiens)
Explore P63316 
Go to UniProtKB:  P63316
PHAROS:  P63316
GTEx:  ENSG00000114854 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63316
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
C2 H3 O2
Query on CA

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.37 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.576α = 90
b = 49.576β = 90
c = 116.041γ = 120
Software Package:
Software NamePurpose
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations