Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding
- Chinese Academy of Sciences, China
Abstract
Mammalian mitochondrial inner membrane fusion is mediated by optic atrophy 1 (OPA1). Under physiological conditions, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (L-OPA1) and a soluble short isoform (S-OPA1). A combination of L-OPA1 and S-OPA1 is essential for efficient membrane fusion; however, the relevant mechanism is not well understood. In this study, we investigate the cryo-electron microscopic structures of S-OPA1–coated liposomes in nucleotide-free and GTPγS-bound states. S-OPA1 exhibits a general dynamin-like structure and can assemble onto membranes in a helical array with a dimer building block. We reveal that hydrophobic residues in its extended membrane-binding domain are critical for its tubulation activity. The binding of GTPγS triggers a conformational change and results in a rearrangement of the helical lattice and tube expansion similar to that of S-Mgm1. These observations indicate that S-OPA1 adopts a dynamin-like power stroke membrane remodeling mechanism during mitochondrial inner membrane fusion.
Data availability
Cryo-EM maps of S-OPA1 196-252 coated tubes have been deposited into Electron Microscopy Data Bank with the accession codes EMD-9901 for the helical reconstruction of nucleotide-free state, EMD-9903 for the tomographic reconstruction of nucleotide-free state and EMD-9902 for the tomographic reconstruction of GTPγS bound state, respectively. Sub-tomogram averaged cryo-EM map of wild type S-OPA1 coated tubes is also deposited with the accession code of EMD-0722. The raw data of GTPase assay in this study has been included as a supporting file.
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Helical reconstruction of S-OPA1 at nucleotide-free stateEMDB Protein Data Bank, EMD- 9901.
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S-OPA1 coated liposome tube at GTPgamaS bound stateEMDB Protein Data Bank, EMD- 9902.
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S-OPA1 coated liposome tube at nucleotide-free stateEMDB Protein Data Bank, EMD- 9903.
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Full length S-OPA1 coated liposome tube at nucleotide-free stateEMDB Protein Data Bank, EMD- 0722.
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Crystal structure of nucleotide-free Mgm1RCSB Protein Data Bank, 6QL4.
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Structure of s-Mgm1 decorating the outer surface of tubulated lipid membranesRCSB Protein Data Bank, 6RZT.
Article and author information
Author details
Funding
National Natural Science Foundation of China (31770794)
- Yan Zhang
Chinese Academy of Sciences (XDB08030202)
- Fei Sun
Ministry of Science and Technology of the People's Republic of China (2017YFA0504700)
- Fei Sun
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Zhang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding
eLife 9:e50294.
https://doi.org/10.7554/eLife.50294
Further reading
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In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5′ end with a 7-methylguanosine (m7G) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5′ end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
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Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure–function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.
