Symmetry alignment of EF-hand

The EF-hand domain is a helix-loop-helix motif, which is usually found in proteins involved in signal transduction by calcium ions {Kawasaki and Kretsinger, 1995, Protein Profile, 2, 297-490}. The EF-hand is observed in many proteins in various structural contexts. EF-hand is the first sequence-motif describing the function and the relationship between tertiary structure and primary structure {Tufty and Kretsinger, 1975, Science, 187, 167-9}. Some EF-hand proteins consist of only EF-hand domains. Many other EF-hand proteins are heterochimeric protein, in which domains other than EF-hand fused to EF-hand domain at either the N-terminal or the C-terminal side {Kawasaki et al., 1998, Biometals, 11, 277-95}. EF-hand motif occurs usually as a pair, EF-lobe, although there are some exception such as the first domain of parvalbumin covers hydrophobic core of the pair of EF-hand {Moews and Kretsinger, 1975, J Mol Biol, 91, 201-25} and the fifth domain of calpain and sorcin, which pairs with the fifth domain of another penta-EF hand protein {Blanchard et al., 1997, Nat Struct Biol, 4, 532-8; Lin et al., 1997, Nat Struct Biol, 4, 539-47}.
All EF-hand domains are inferred to have evolved from a single ancestral helix-loop-helix motif by duplication and fusion {Moncrief et al., 1990, J Mol Evol, 30, 522-62; Nakayama et al., 1992, J Mol Evol, 34, 416-48}.
The two EF-hands of an EF-lobe are related by a pseudo-two fold axis. This axis is perpendicular to the line connecting the centres of mass of the two EF-hands; it reflects the duplication and fusion of a gene encoding a single EF-hand.
One can view several features of the EF-hand structure relative to this axis (z-axis). Using the coordinate system defined by the plane with the z-axis and the line connecting centers of mass (x-axis), we could describe the structural features of an EF-lobe without a reference structure for the superposition. The interface between the two EF-hands of an EF-lobe defines a plane that includes the z-axis and the y-axis.

View aligned EF-hand structure on our server
View aligned EF-hand structure by uploading output pdb file of HVM server

--- HVM server ---

Geometrical Analysis of EF-hand --- Calculation of pseudo-two fold axis ---

Hiroshi Kawasaki
Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University,
Suehiro-cho 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan

Robert H. Kretsinger
Department of Biology, University of Virginia,
Charlottesville, VA, 22901, USA