Knowledge-based real-space explorations for low-resolution structure determination.
The accurate and effective interpretation of low-resolution data in X-ray crystallography is becoming increasingly important as structural initiatives turn toward large multiprotein complexes. Substantial challenges remain due to the poor information content and ambiguity in the interpretation of electron density maps at low resolution. Here, we describe a semiautomated procedure that employs a restraint-based conformational search algorithm, RAPPER, to produce a starting model for the structure determination of ligase interacting factor 1 in complex with a fragment of DNA ligase IV at low resolution. The combined use of experimental data and a priori knowledge of protein structure enabled us not only to generate an all-atom model but also to reaffirm the inferred sequence registry. This approach provides a means to extract quickly from experimental data useful information that would otherwise be discarded and to take into account the uncertainty in the interpretation--an overriding issue for low-resolution data.
Furnham
Nicholas
N
Sanger Building, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. nick@cryst.bioc.cam.ac.uk
Doré
Andrew S
AS
Chirgadze
Dimitri Y
DY
de Bakker
Paul I W
PI
Depristo
Mark A
MA
Blundell
Tom L
TL
D000465:Algorithms; D018360:Crystallography, X-Ray / Q000379:methods*; D000072481:DNA Ligase ATP; D011088:DNA Ligases / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D012815:Signal Processing, Computer-Assisted
D004268:DNA-Binding Proteins; C000607891:DNL4 protein, S cerevisiae; C114091:LIF1 protein, S cerevisiae; D046912:Multiprotein Complexes; D029701:Saccharomyces cerevisiae Proteins; D011088:DNA Ligases; D000072481:DNA Ligase ATP