Phased translation function revisited

Structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches

Boris V. Strokopytov, Alexander Fedorov, Nicole M. Mahoney, Michael Kessels, David G. Drubin, Steven C. Almo

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

A modified molecular-replacement method is described that makes use of six-dimensional searches and the phased translation function, providing a systematic examination of all possible search-model orientations in an experimental electron-density map. As an example, the structure solution of the cofilin-homology domain of the Saccharomyces cerevisiae actin-binding protein 1 (ABP1) is presented in detail. Additional examples are presented in which these tools have significantly aided structure solutions in a variety of contexts. These results suggest that this approach might be of widespread utility for challenging structures involving weak phase information, complex asymmetric units and search models with weak structural homology. Furthermore, this approach supports an exhaustive molecular-replacement strategy in cases where an appropriate search model cannot readily be identified on the basis of sequence homology. The fully automated web-based implementation of this phased translation function is described.

Original languageEnglish (US)
Pages (from-to)285-293
Number of pages9
JournalActa Crystallographica Section D: Biological Crystallography
Volume61
Issue number3
DOIs
StatePublished - Mar 2005

Fingerprint

Actin Depolymerizing Factors
Microfilament Proteins
Fungal Proteins
yeast
homology
Yeast
Saccharomyces cerevisiae Proteins
proteins
Sequence Homology
saccharomyces
Electrons
Carrier concentration
examination

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Condensed Matter Physics
  • Structural Biology

Cite this

Phased translation function revisited : Structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches. / Strokopytov, Boris V.; Fedorov, Alexander; Mahoney, Nicole M.; Kessels, Michael; Drubin, David G.; Almo, Steven C.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 61, No. 3, 03.2005, p. 285-293.

Research output: Contribution to journalArticle

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