Dr Jon Agirre

Royal Society University Research Fellow

Tel: 01904 32 8252  Office: B/K/065 (Biology, Campus West)
Email: jon.agirre@york.ac.uk

ORCID iD iconorcid.org/0000-0002-1086-0253

A new methodological foundation for carbohydrate structure determination

Carbohydrate structure

Sugars - little image

‌‌I work with Kevin CowtanGideon Davies and Keith Wilson on the development of new methods for carbohydrate structure detection, refinement and validation. Using a YSBL-designed fingerprinting engine, we can create syntheses of different sugars and their environment, and then use that information for detecting features in a crystallographic or cryoEM map. This is precisely what the Sails software does. After they are built, structures can be refined and validated with the aid of Privateer, the first sugar-specific validation software to check ring conformation, stereochemistry, linkage torsions, nomenclature and fit to unbiased electron density maps. Additionally, Privateer produces vector diagrams (SVG) for glycans - these are compliant with the 'Essentials of Glycobiology 3rd edition' nomenclature. Privateer can be obtained through CCP4.

Glycan visualisation

A figure from the Glycoblocks paper

Together with Stuart McNicholas, and with key input from Gideon Davies (and his group) and Keith Wilson, we have developed Glycoblocks, which is a schematic 3D representation for glycans and their interactions.‌ This representation is available within CCP4mg, the CCP4 molecular graphics program. As both are part of the CCP4 suite, CCP4mg can use the interactive 2D glycan diagrams - compliant with the 'Essentials of Glycobiology 3rd edition' nomenclature - and validation information generated by Privateer.

Automation (crystallography & cryoEM)

I work with Kevin Cowtan on the development of new methods to aid in macromolecular structure solution from X-ray Crystallography and cryoEM data. We are currently engaged in developing methods for model-free refinement, fast B-factor refinement and estimation of local map resolution, for both X-ray crystallography and cryoEM. I also share interests and projects with a number of YSBL crewmates, including Eleanor Dodson (development of pipelines and tasks for CCP4i2), Stuart McNicholas (Clipper-python module), and Huw Jenkins and Christian Roth (ab-initio structure solution).

Selected publications

  • Privateer: software for the conformational validation of carbohydrate structures.
    Jon Agirre, Javier Iglesias-Fernández, Carme Rovira, Gideon Davies, Keith Wilson and Kevin Cowtan. Nature Structural & Molecular Biology, 2015, 22(11), 833-834.
  • Carbohydrate anomalies in the PDB. 
    Jon Agirre, Gideon Davies, Keith Wilson and Kevin Cowtan. Nature Chemical Biology, 2015, 11, 303.
  • Glycoblocks: a schematic 3D representation for glycans and their interactions.
    Stuart McNicholas and Jon Agirre. Acta Crystallographica, 2017, D73, 187-194.
  • Strategies for carbohydrate model building, refinement and validation.
    Jon Agirre. Acta Crystallographica D, 2017, D73, 171-186.
  • Carbohydrate structure: the rocky road to automation.
    Jon Agirre, Gideon Davies, Keith Wilson and Kevin Cowtan. Current Opinion in Structural Biology, 2017, 44, 39-47.
  • Automating tasks in protein structure determination with the Clipper Python module.
    Stuart McNicholas, Tristan Croll, Tom Burnley, Colin Palmer, Scott Hoh, Huw Jenkins, Eleanor Dodson, Kevin Cowtan and Jon Agirre. Protein Science, 2018, 27(1), 207-216.
  • Forty years of collaborative computational crystallography.
    Jon Agirre and Eleanor Dodson. Protein Science, 2018, 27(1), 202-206.

 Upcoming conferences, workshops and courses

Want to catch up with me? Here is a list of times and places where we can meet and discuss

  • CCP-EM Spring Symposium IV (Keele)
    11-12th April 2018 (as a participant)
  • Royal Society of Chemistry Carbohydrate group Early Career Researcher Meeting (Keele) 
    12-13th April 2018 (as a speaker)
  • Royal Society course - Writing about your research (London)
    9th May 2018 (as a participant)
  • CCP4 Working group 2 meeting (London) 
    6th June 2018 (as a speaker)
  • Royal Society course - Media skills (London)
    18th October 2018 (as a participant)
  • Simulations for the Experimentalist and the Industrialist course (Diamond Light Source)
    6-7th November 2018 (as a participant)



PhD vacancies

A new methodological foundation for carbohydrate model building, validation and representation (self-funded project) - open to all applicants who are able to fund their own studies. More information here.

Twitter updates

ORCID iD iconorcid.org/0000-0002-1086-0253

Funding and support

My group's activities are supported by:

The Royal Society - logo

CCP-em logo