11KH

Rabbit 80S with IFRD2 and LARP1, 40S head-swiveled

This is a non-PDB format compatible entry.

Summary for 11KH

• Entry DOI: 10.2210/pdb11kh/pdb
• EMDB information: 75768
• Descriptor: Small ribosomal subunit protein uS2, 60S ribosomal protein L5, large ribosomal subunit protein eL6, ... (86 entities in total)
• Functional Keywords: ribosome, hibernation, in extracto cryo em, rabbit
• Biological source: Oryctolagus cuniculus (rabbit); More
• Total number of polymer chains: 85
• Total formula weight: 5342609.74

Authors

Seraj, Z.,Zottig, X.,Huang, C.H.,Loveland, A.B.,Diggs, S.,Sholi, E.,Grigorrieff, N.,Korostelev, A.A. (deposition date: 2026-02-28, release date: 2026-09-02, Last modification date: 2026-09-16)

Primary citation

Seraj, Z.,Zottig, X.,Huang, C.,Loveland, A.B.,Diggs, S.,Sholi, E.,Grigorieff, N.,Korostelev, A.A.
In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles.
Elife, 15:-, 2026

PubMed Abstract: Cryogenic electron microscopy (cryo-EM) made impressive progress in resolving cellular macromolecules and their detailed interactions. Single-particle cryo-EM traditionally relies on purified macromolecules and lacks the complexity of cellular environments, whereas cryo-EM and cryogenic electron tomography (cryo-ET) require extensive sample preparation and data acquisition, presenting challenges in achieving high resolution. We describe cryo-EM of cellular lysates- cryo-EM-allowing the flexibility and high-resolution of cryo-EM in the context of cellular components. High-resolution 2D template matching (2DTM) yields ~2.2 Å maps of the mammalian translational apparatus. Elongating ribosome abundances in primate cell lines (MCF-7 and BSC-1) and rabbit reticulocyte lysates range from ~70% to ~10%, reflecting translational stress responses. Non-translating (hibernating) ribosomes carrying no mRNA feature numerous proteins shielding ribosomal functional centers. Elongation factor 2 (eEF2) is the most abundant hibernation factor bound to >95% of 80S ribosomes and, unexpectedly, to 60S subunits. eEF2•GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature La-related protein 1 (LARP1) involved in initiation and mTOR signaling, eIF5A implicated in elongation and termination, and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution.

PubMed: 42689549
DOI: 10.7554/eLife.110114

Experimental method

ELECTRON MICROSCOPY (3.1 Å)