In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity
Spyridon Gourdoupis, Veronica Nasta, Simone Ciofi-Baffoni, Lucia Banci and Vito Calderone [1]
Molecular Tour
IBA57 is a 325-residue human protein which localizes to the mitochondrion and is part of the iron-sulfur cluster assembly pathway [2], [3].
The maturation of mitochondrial iron-sulfur proteins requires a complex protein machinery. In the late steps of this machinery, a [2Fe-2S] cluster is converted into a [4Fe-4S] cluster. Human IBA57 protein acts in this step as an iron-sulfur cluster assembly component along with ISCA1 and ISCA2 [4], [5], [6], [7].
The structure of this protein was still unknown and the closest homologue whose structure was determined showed 25% sequence homology only (which made molecular replacement in principle unlikely to be successful). For this reason, experimental phasing was the most likely way to solve it.
This paper (DOI 10.1107/S2059798319000214) describes the approach used to solve in-house the structure of human IBA57 through 5-amino-2,4,6-triiodoisophthalic acid (I3C) high energy remote SAD-phasing. Multiple orientations (each of them corresponding to a different run) of the same P1 (triclinic) crystal have been exploited to acquire sufficient real data multiplicity for successful phasing and thus minimizing the difficulties of merging datasets coming from different crystals.
Screenshot of IBA57 crystals
It is also described how the joint use of this I3C derivative and of an in-house native dataset through a SIRAS approach decreases the data multiplicity needed for phasing by almost 50%.
Furthermore, it is illustrated that there is a clear data multiplicity threshold value for success and failure in phasing and how adding further data does not significantly affect substructure solution and model building. The multiplicity threshold for successful phasing appeared, in fact, to be around five, independent of the combination of datasets (runs) used. This value can be reduced to about half through SIRAS by exploiting the isomorphous differences with a second native dataset reaching a successful multiplicity value of less than three.
To our knowledge, this is the only structure present in the PDB which has been solved in-house, through remote SAD, in space group P1 and using one crystal only. All the raw data used, deriving from the different orientations (runs), have been deposited to Zenodo (DOI 10.5281/zenodo.2531553)[8] both for educational purposes and to enable other crystallographers to improve methods for data processing and structure solution and thus to benefit from these findings.
At the time of structure solution coordinates and structure factors were deposited and released in the Protein Data Bank under the accession codes 5oli (for the in-house I3C derivative) and 6esr (for the higher resolution synchrotron structure); at the time of writing the manuscript both entries have been re-refined in order to optimize model quality and statistics and so they have been superseded by 6qe4 and 6qe3 respectively.
with the residues for which even the main chain electron density is very poor if not absent at all highlighted in red (53-59, 61, 88-92, 115-118, 138-147, 262, 296-300, 306-311).
between 6esr (red) and 5oli (green) secondary structures. It appears that, in the case of 6esr, there is a slight loss in secondary structure elements (mainly β-strands in the N-terminus region) with respect to 5oli and there is the appearance of a very short 3/10 helix around residue 90. It must be pointed out anyway that those regions mostly correspond to the regions in which electron density is very weak and thus model tracing can be quite approximate.
- . Water molecules are shown as red spheres.
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PDB references: Re-refinement of 6ESR human IBA57 at 1.75 A resolution 6qe3; Re-refinement of 5OLI human IBA57-I3C 6qe4.
References
- ↑ Gourdoupis S, Nasta V, Ciofi-Baffoni S, Banci L, Calderone V. In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity. Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):317-324. doi:, 10.1107/S2059798319000214. Epub 2019 Feb 28. PMID:30950402 doi:http://dx.doi.org/10.1107/S2059798319000214
- ↑ Rouault TA. Mammalian iron-sulphur proteins: novel insights into biogenesis and function. Nat Rev Mol Cell Biol. 2015 Jan;16(1):45-55. doi: 10.1038/nrm3909. Epub 2014 Nov , 26. PMID:25425402 doi:http://dx.doi.org/10.1038/nrm3909
- ↑ Andreini C, Rosato A, Banci L. The Relationship between Environmental Dioxygen and Iron-Sulfur Proteins Explored at the Genome Level. PLoS One. 2017 Jan 30;12(1):e0171279. doi: 10.1371/journal.pone.0171279., eCollection 2017. PMID:28135316 doi:http://dx.doi.org/10.1371/journal.pone.0171279
- ↑ Brancaccio D, Gallo A, Mikolajczyk M, Zovo K, Palumaa P, Novellino E, Piccioli M, Ciofi-Baffoni S, Banci L. Formation of [4Fe-4S] clusters in the mitochondrial iron-sulfur cluster assembly machinery. J Am Chem Soc. 2014 Nov 19;136(46):16240-50. doi: 10.1021/ja507822j. Epub 2014, Nov 7. PMID:25347204 doi:http://dx.doi.org/10.1021/ja507822j
- ↑ Brancaccio D, Gallo A, Piccioli M, Novellino E, Ciofi-Baffoni S, Banci L. [4Fe-4S] Cluster Assembly in Mitochondria and Its Impairment by Copper. J Am Chem Soc. 2017 Jan 18;139(2):719-730. doi: 10.1021/jacs.6b09567. Epub 2017, Jan 3. PMID:27989128 doi:http://dx.doi.org/10.1021/jacs.6b09567
- ↑ Ciofi-Baffoni S, Nasta V, Banci L. Protein networks in the maturation of human iron-sulfur proteins. Metallomics. 2018 Jan 24;10(1):49-72. doi: 10.1039/c7mt00269f. PMID:29219157 doi:http://dx.doi.org/10.1039/c7mt00269f
- ↑ Gourdoupis S, Nasta V, Calderone V, Ciofi-Baffoni S, Banci L. IBA57 Recruits ISCA2 to Form a [2Fe-2S] Cluster-Mediated Complex. J Am Chem Soc. 2018 Oct 31;140(43):14401-14412. doi: 10.1021/jacs.8b09061. Epub, 2018 Oct 17. PMID:30269484 doi:http://dx.doi.org/10.1021/jacs.8b09061
- ↑ In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity. Zenodo January 4, 2019 doi:https://dx.doi.org/10.5281/zenodo.2531553
