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Open Access Highly Accessed Research article

A three-dimensional topology of complex I inferred from evolutionary correlations

Philip R Kensche12*, Isabel Duarte12 and Martijn A Huynen12

Author Affiliations

1 Center for Molecular and Biomolecular Informatics / Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, Nijmegen, HB, 6500, The Netherlands

2 Netherlands Bioinformatics Centre, Geert Grooteplein 28, Nijmegen, GA, 6525, The Netherlands

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BMC Structural Biology 2012, 12:19  doi:10.1186/1472-6807-12-19

Published: 3 August 2012

Additional files

Additional file 1:

Microsoft Word 97 Document. Table of human complex I members and query sequence identifiers and Shepard diagrams for the three discussed models [1,17][94-100].

Format: DOC Size: 553KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 2:

Zip-compressed FASTA alignment files. Manually curated and unfiltered alignments. The FASTA header lines contain (1) a short sequence identifier consisting of a number and the abbreviated species name and (2) a long sequence identifier with the number written between the genus and epithet of the species name. Sequence gaps are indicated by '-'. Subunits NADH3, NADH4L, and NADH6 were combined ("nadh34L6").

Format: ZIP Size: 2.8MB Download file

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Additional file 3:

Zip-compressed New Hampshire eXtended (NHX) tree files. Gene trees.

Format: ZIP Size: 127KB Download file

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Additional file 4:

Tabulator delimited text file. Matrix of pairwise co-evolutionary distances.

Format: TSV Size: 32KB Download file

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Additional file 5:

VRML97 format. Interactive visualization of the evolutionary configuration. The predicted subunit centers are labeled by the abbreviations used in the article and color-coded according to sub-complex membership [see Additional file 1]. Specifically, most subunits are abbreviated by omitting the "NADH" or "NDUF" prefix, with the exception of NUBPL, C20orf7, C8orf38, and C2orf56 that are abbreviated to N, O7, O38, and O56, respectively. The sub-complexes are Iλ (blue), Iα-λ (white), Iγ (yellow), and Iβ (red). Subunits without sub-complex association are shown in purple. You can display the VRML97 file of the configuration using a VRML viewer like Flux Player (Windows; http://mediamachines.wordpress.com/flux-player-and-flux-studio/ webcite) or freewrl (Windows, Linux, Mac; http://freewrl.sourceforge.net/ webcite).

Format: WRL Size: 49KB Download file

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