5TNC

REFINED CRYSTAL STRUCTURE OF TROPONIN C FROM TURKEY SKELETAL MUSCLE AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 A resolution.

Herzberg, O.James, M.N.

(1988) J.Mol.Biol. 203: 761-779


  • PubMed Abstract: 
  • The crystal structure of troponin C from turkey skeletal muscle has been refined at 2.0 A resolution (1 A = 0.1 nm). The resulting crystallographic R factor (R = sigma[[Fo[-[Fc[[/sigma[Fo[, where [Fo[ and [Fc[ are the observed and calculated structur ...

    The crystal structure of troponin C from turkey skeletal muscle has been refined at 2.0 A resolution (1 A = 0.1 nm). The resulting crystallographic R factor (R = sigma[[Fo[-[Fc[[/sigma[Fo[, where [Fo[ and [Fc[ are the observed and calculated structure factor amplitudes) is 0.155 for the 8054 reflections with intensities I greater than or equal to 2 sigma(I) within the 10 A to 2.0 A resolution range. With 66% of the residues in helical conformation, troponin C provides a good sample for helix analysis. The mean alpha-helix dihedral angles (phi, psi = -62 degrees, -42 degrees) agree with values observed for helical regions in other proteins. The helices are all curved and/or kinked. In particular, the 31 amino acid long inter-domain helix is smoothly curved, with a rather large radius of curvature of 137 A. Helix packing is different in the Ca2+-free domain (N-terminal) and the Ca2+-bound domain (C-terminal). The inter-helix angles for the two helix-loop-helix motifs in the regulatory domain are 133 degrees and 151 degrees, whereas the value for the two motifs in the C-terminal domain is 110 degrees, as observed in the EF-hands of parvalbumin. These differences affect the packing of the respective hydrophobic cores of each domain, in particular the disposition of aromatic rings. Pairwise arrangement of Ca2+-binding loops is common to both states, but the conformation is markedly different. Conversion of one to the other can be achieved by small cumulative changes of main-chain dihedral angles. The integrity of loop structure is maintained by numerous electrostatic interactions. Both salt bridges and carboxyl-carboxylate interactions are observed in TnC. There are more intramolecular (9) than intermolecular (1) salt bridges. Carboxyl-carboxylate interactions occur because the pH of the crystals is 5.0 and there is a multitude of aspartate and glutamate residues. One is intramolecular and four are intermolecular. Polar side-chain interactions occur more commonly with main-chain carbonyls and amides than with other polar side-chains. These interactions are mostly short range, and are similar to those observed in other proteins with one exception: negatively charged side-chains interact more frequently with main-chain carbonyl oxygen atoms. However, out of 19 such interactions, 10 involve oxygen atoms of the Ca2+ ligands. These unfavorable interactions are compensated by the favorable interactions with the Ca2+ ions and with main-chain amides. They are a trivial consequence of the tight fold of the Ca2+-binding loops.


    Related Citations: 
    • Crystallographic Data for Troponin C from Turkey Skeletal Muscle
      Herzberg, O.,Hayakawa, K.,James, M.N.G.
      (1984) J.Mol.Biol. 172: 345
    • Calcium Binding to Skeletal Muscle Troponin C and the Regulation of Muscle Contraction
      Herzberg, O.,Moult, J.,James, M.N.G.
      (1986) Ciba Found.Symp. 122: 120
    • Structure of the Calcium Regulatory Muscle Protein Troponin-C at 2.8 Angstroms Resolution
      Herzberg, O.,James, M.N.G.
      (1985) Nature 313: 653
    • The Crystal Structure of Troponin C from Turkey Skeletal Muscle at 2.8 Angstroms Resolution
      Herzberg, O.,James, M.N.G.
      (1984) Acta Crystallogr.,Sect.A 40: C37
    • A Model for the Ca2+-Induced Conformational Transition of Troponin C. A Trigger for Muscle Contraction
      Herzberg, O.,Moult, J.,James, M.N.G.
      (1986) J.Biol.Chem. 261: 2638
    • Crystallographic Determination of Lanthanide Ion Binding to Troponin C
      Herzberg, O.,James, M.N.G.
      (1986) FEBS Lett. 199: 279
    • Conformational Flexibility of Troponin C
      Herzberg, O.,Moult, J.,James, M.N.G.
      (1987) Calcium-Binding Proteins in Health and Disease --: 312
    • Molecular Structure of Troponin C and its Implications for the Ca2+ Triggering of Muscle Contraction
      Herzberg, O.,Moult, J.,James, M.N.G.
      (1987) Methods Enzymol. 139: 610
    • Common Structural Framework of the Two Ca2+(Slash)Mg2+ Binding Loops of Troponin C and Other Ca2+ Binding Proteins
      Herzberg, O.,James, M.N.G.
      (1985) Biochemistry 24: 5298


    Organizational Affiliation

    Medical Research Council of Canada Group, University of Alberta, Edmonton.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TROPONIN-C
A
162Meleagris gallopavoMutation(s): 0 
Gene Names: TNNC2
Find proteins for P10246 (Meleagris gallopavo)
Go to Gene View: TNNC2
Go to UniProtKB:  P10246
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.550α = 90.00
b = 66.550β = 90.00
c = 60.910γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-10-09
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance