7OYD

Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b

This is a non-PDB format compatible entry.

Summary for 7OYD

• Entry DOI: 10.2210/pdb7oyd/pdb
• EMDB information: 13114
• Descriptor: Ribosomal protein uL1, 40S ribosomal protein S27, 60S ribosomal protein L4, ... (85 entities in total)
• Functional Keywords: translation, embryo, zebrafish, maternal, dap1, dap1b, habp4, eif5a, eef2b, ribosome
• Biological source: Danio rerio (zebrafish); More
• Total number of polymer chains: 83
• Total formula weight: 3579110.89

Authors

Leesch, F.,Lorenzo-Orts, L.,Grishkovskaya, I.,Kandolf, S.,Belacic, K.,Meinhart, A.,Haselbach, D.,Pauli, A. (deposition date: 2021-06-24, release date: 2022-07-20, Last modification date: 2025-10-01)

Primary citation

Leesch, F.,Lorenzo-Orts, L.,Pribitzer, C.,Grishkovskaya, I.,Roehsner, J.,Chugunova, A.,Matzinger, M.,Roitinger, E.,Belacic, K.,Kandolf, S.,Lin, T.Y.,Mechtler, K.,Meinhart, A.,Haselbach, D.,Pauli, A.
A molecular network of conserved factors keeps ribosomes dormant in the egg.
Nature, 613:712-720, 2023

PubMed Abstract: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.

PubMed: 36653451
DOI: 10.1038/s41586-022-05623-y

Experimental method

ELECTRON MICROSCOPY (2.3 Å)