A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study

Acta Crystallographica. Section D, Structural Biology
Adam D CrawshawPaula S Salgado

Abstract

Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.

References

Oct 24, 2003·Acta Crystallographica. Section D, Biological Crystallography·Garry Taylor
Oct 24, 2003·Acta Crystallographica. Section D, Biological Crystallography·Elspeth Garman, James W Murray
Jan 1, 1993·Acta Crystallographica. Section D, Biological Crystallography·A T Brünger
Oct 20, 2004·Molecular Microbiology·Rolf KöhlerWolfram Welte
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·E Krissinel, K Henrick
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Elspeth F Garman, Robin Leslie Owen
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Philip Evans
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
May 16, 2007·Molecular Microbiology·Andrea G O ManettiImmaculada Margarit
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Sep 26, 2007·Proceedings of the National Academy of Sciences of the United States of America·Sophie HelaineKatrina T Forest
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Philip Evans, Airlie McCoy
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Fei LongGarib N Murshudov
Feb 6, 2008·Current Opinion in Structural Biology·Lisa Craig, Juliana Li
Nov 20, 2008·Acta Crystallographica. Section D, Biological Crystallography·Daniel J RigdenMartyn D Winn
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Jul 31, 2009·The Journal of Biological Chemistry·Konstantin V KorotkovWim G J Hol
Oct 16, 2009·International Journal of Antimicrobial Agents·Haihui HuangCarl Erik Nord
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Alexei Vagin, Alexei Teplyakov
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·Garry L Taylor
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·George M Sheldrick
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
May 12, 2010·Nucleic Acids Research·Liisa Holm, Päivi Rosenström
Jul 8, 2010·Acta Crystallographica. Section D, Biological Crystallography·Grzegorz BujaczAnna Bujacz
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Gwyndaf EvansRobin L Owen
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·T Geoff G BattyeAndrew G W Leslie
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Gábor Bunkóczi, Randy J Read
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Garib N MurshudovAlexei A Vagin
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·S McNicholasM E M Noble
Mar 27, 2012·Journal of Bacteriology·Subramaniapillai KolappanLisa Craig
Apr 3, 2012·Nature Reviews. Microbiology·Konstantin V KorotkovWim G J Hol
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Ethan A Merritt
Nov 16, 2012·Acta Crystallographica. Section D, Biological Crystallography·Jaclyn BibbyDaniel J Rigden
Jun 26, 2013·Acta Crystallographica. Section D, Biological Crystallography·Philip R Evans, Garib N Murshudov
Sep 6, 2013·Microbiology and Molecular Biology Reviews : MMBR·Stephen Melville, Lisa Craig
Sep 17, 2013·Nature Methods·Massimo SammitoIsabel Usón
Dec 24, 2013·The Journal of Biological Chemistry·Kurt H PiepenbrinkEric J Sundberg
Jul 10, 2014·Acta Crystallographica. Section D, Biological Crystallography·Jimin WangYorgo Modis
Oct 8, 2014·Acta Crystallographica. Section D, Biological Crystallography·Richard J GildeaGraeme Winter

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
PISA
NMR

Software Mentioned

PDBe
MolProbity
BALBES
CHAINSAW
Phaser
ARP
PISA
wARP
PDBeFold
Buccaneer

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.