Validation of Cryo-EM Structure of IP3R1 Channel

About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure...

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Bibliographic Details
Published in:Structure (London) 2013-06, Vol.21 (6), p.900-909
Main Authors: Murray, Stephen C., Flanagan, John, Popova, Olga B., Chiu, Wah, Ludtke, Steven J., Serysheva, Irina I.
Format: Article
Language:English
Subjects:
Channels
Criteria
Cryoelectron Microscopy - methods
Crystallography, X-Ray
Inositol 1,4,5-Trisphosphate Receptors - chemistry
Molecular machines
Molecular structure
Protein Conformation
Similarity
Software packages
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Summary:About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines. •Five different reconstruction algorithms agree on the IP3R1 quaternary structure•IP3R1 quaternary structure is validated by tilt-pair analysis•Resolution of the IP3R1 map has been assessed using the gold standard criterion To prove the veracity of their recent cryo-EM structure of IP3R1, Murray et al. apply several validation methods, including the “gold standard” resolution test. This is part of an effort in the community to establish tools and standards for better identifying errors in cryo-EM structures by single-particle approach.
ISSN:0969-2126
1878-4186
DOI:10.1016/j.str.2013.04.016