Problem cryo-ET structure alert. A recent paper by Lange et al. in @natcellbio.nature.com (tinyurl.com/38s6a4dn) reported an unusual-looking model of the prohibitin complex in situ. We asked: how was this structure generated? Our reanalysis offers an explanation: tinyurl.com/mszdtwxx 🧵 - ThreadSky

jimhurley.bsky.social • 8 days ago

Problem cryo-ET structure alert. A recent paper by Lange et al. in @natcellbio.nature.com (https://tinyurl.com/38s6a4dn) reported an unusual-looking model of the prohibitin complex in situ. We asked: how was this structure generated? Our reanalysis offers an explanation: https://tinyurl.com/mszdtwxx 🧵

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jimhurley.bsky.social•8 days ago

Cryo-FIB milling and in situ cryo-ET are opening immensely exciting windows to structural-level insight in the cellular context. At the same time, tools like AlphaFold have made protein structure prediction widely accessible.

jimhurley.bsky.social•8 days ago

This is exciting progress. But with new methods come new pitfalls. As Richard Henderson noted in 2013, “one must not underestimate the ingenuity of humans to invent new ways to deceive themselves.”

jimhurley.bsky.social•8 days ago

The Lange et al. paper presented a model of the prohibitin complex with 11 well-separated radial spokes, unlike any known structure of homologous proteins - a big warning sign. The shape was like an 11-armed octopus, with large gaps between the spokes and no physical mechanism holding them together.

jimhurley.bsky.social•8 days ago

To be convincing, a model should fill the density and should have physically plausible contacts between the subunits, which will hold the subunits in place, like this (https://rcsb.org 9O6S):

jimhurley.bsky.social•8 days ago

Prohibitin is a heterodimer of PHB1 and PHB2. Yet there was not enough density to dock 11 PHB1:2 dimers. A asymmetric model consisting of 6 copies of one subunit and 5 of another was docked into the density. This is inconsistent with the symmetry assumptions, raising further structural concerns.

jimhurley.bsky.social•8 days ago

In our own analysis (https://tinyurl.com/66we8sn5), we found that in healthy cells, prohibitin is in a predominantly open, asymmetric state. Forcing 11-fold symmetry onto this heterogeneous population can produce densities resembling the published density and replicate the model of the 11-armed octopus.

pascalalbanese.bsky.social•8 days ago

Thanks Jim for this Alert. About XL-MS mapping using our tool XMAS: in fig 2C you are plotting the same restraint multiple times (aligned grey dots). To avoid this and show only the shortest in the oligomer you can hit “analyze>find shortest>0Å difference” (default cutoff is 2Å). Cheers :)

jimhurley.bsky.social•7 days ago

Thanks for alerting us. Kevin Rose in the lab recalculated using this option. The plots are sparser but the gist is the same.

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