{"entity": "researcher", "timestamp": "2026-07-12T08:56:55.534Z", "family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "affiliations": ["Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.", "Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582"}}, "publications": [{"entity": "publication", "iuid": "2a1aa60f79b748bab652fae28b784691", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a1aa60f79b748bab652fae28b784691.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a1aa60f79b748bab652fae28b784691"}}, "title": "Mechanism of mitoribosomal small subunit biogenesis and preinitiation.", "authors": [{"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Khawaja", "given": "Anas", "initials": "A"}, {"family": "Laptev", "given": "Ivan", "initials": "I", "orcid": "0000-0002-1893-2055", "researcher": {"href": "https://publications.scilifelab.se/researcher/6316213061d54141a39ba6fdbd47d535.json"}}, {"family": "Cipullo", "given": "Miriam", "initials": "M"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Sergiev", "given": "Petr", "initials": "P", "orcid": "0000-0001-8866-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b196a60aa2470caf698cb35fba2ebd.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "606", "issue": "7914", "pages": "603-608", "issn-l": "0028-0836"}, "abstract": "Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.", "doi": "10.1038/s41586-022-04795-x", "pmid": "35676484", "labels": {"Global Proteomics and Proteogenomics": "Service", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9200640"}, {"db": "pii", "key": "10.1038/s41586-022-04795-x"}], "notes": [], "created": "2022-11-24T11:48:58.764Z", "modified": "2022-12-02T09:59:24.357Z"}, {"entity": "publication", "iuid": "3bd14e6b3d1244cc89745dc4f8dd7e15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bd14e6b3d1244cc89745dc4f8dd7e15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bd14e6b3d1244cc89745dc4f8dd7e15"}}, "title": "Mechanism of membrane-tethered mitochondrial protein synthesis.", "authors": [{"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Andr\u00e9ll", "given": "Juni", "initials": "J", "orcid": "0000-0003-2313-9155", "researcher": {"href": "https://publications.scilifelab.se/researcher/be8a8574a94e42e18cf54c207ec66643.json"}}, {"family": "Choi", "given": "Austin", "initials": "A", "orcid": "0000-0002-5476-4183", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf75934f5bf04d41b03080f6008fbec7.json"}}, {"family": "Richter", "given": "Uwe", "initials": "U", "orcid": "0000-0002-0724-6957", "researcher": {"href": "https://publications.scilifelab.se/researcher/58bed66cedc54c168ef5b31015dc9a45.json"}}, {"family": "Maiti", "given": "Priyanka", "initials": "P", "orcid": "0000-0003-4207-0341", "researcher": {"href": "https://publications.scilifelab.se/researcher/9effd1f62d5a48c1894202af7ea7fba4.json"}}, {"family": "Best", "given": "Robert B", "initials": "RB", "orcid": "0000-0002-7893-3543", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a43cec408bf4353b6d89044c726948d.json"}}, {"family": "Barrientos", "given": "Antoni", "initials": "A", "orcid": "0000-0001-9018-3231", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a9331fc2df454c9c6e288f70c8c976.json"}}, {"family": "Battersby", "given": "Brendan J", "initials": "BJ", "orcid": "0000-0002-8136-2753", "researcher": {"href": "https://publications.scilifelab.se/researcher/39526080fcaf4ee38c1c6dca430ac4e4.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2021-02-19", "journal": {"title": "Science", "issn": "1095-9203", "volume": "371", "issue": "6531", "pages": "846-849", "issn-l": "0036-8075"}, "abstract": "Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery.", "doi": "10.1126/science.abe0763", "pmid": "33602856", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "371/6531/846"}, {"db": "pmc", "key": "PMC7610362"}, {"db": "mid", "key": "EMS117578"}], "notes": [], "created": "2021-12-10T06:53:33.590Z", "modified": "2021-12-10T06:54:03.496Z"}, {"entity": "publication", "iuid": "c66db214519348c0863eeb3e089bbccc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c66db214519348c0863eeb3e089bbccc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c66db214519348c0863eeb3e089bbccc"}}, "title": "Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.", "authors": [{"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Naschberger", "given": "Andreas", "initials": "A"}, {"family": "Mortezaei", "given": "Narges", "initials": "N"}, {"family": "Herrmann", "given": "Johannes M", "initials": "JM", "orcid": "0000-0003-2081-4506", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d45f53a0781428291e45ebb9ac8a372.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2020-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5187", "issn-l": "2041-1723"}, "abstract": "Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.", "doi": "10.1038/s41467-020-18830-w", "pmid": "33056988", "labels": {"Cryo-EM": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18830-w"}, {"db": "pmc", "key": "PMC7560712"}], "notes": [], "created": "2020-10-14T14:19:09.292Z", "modified": "2021-11-10T12:44:48.768Z"}, {"entity": "publication", "iuid": "8e84f5a3ca5548628b22e3d122c5eed6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e84f5a3ca5548628b22e3d122c5eed6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e84f5a3ca5548628b22e3d122c5eed6"}}, "title": "Distinct pre-initiation steps in human mitochondrial translation.", "authors": [{"family": "Khawaja", "given": "Anas", "initials": "A"}, {"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Remes", "given": "Cristina", "initials": "C"}, {"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Yukhnovets", "given": "Olessya", "initials": "O"}, {"family": "H\u00f6fig", "given": "Henning", "initials": "H", "orcid": "0000-0003-0506-783X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5d914f8854e4010949124154dfa1539.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}], "type": "journal article", "published": "2020-06-10", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "2932", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.", "doi": "10.1038/s41467-020-16503-2", "pmid": "32522994", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16503-2"}, {"db": "pmc", "key": "PMC7287080"}], "notes": [], "created": "2020-06-20T05:51:40.998Z", "modified": "2021-11-10T12:50:19.697Z"}, {"entity": "publication", "iuid": "12fa8cdef0e741259e14edbd8e9cb2df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fa8cdef0e741259e14edbd8e9cb2df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fa8cdef0e741259e14edbd8e9cb2df"}}, "title": "Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.", "authors": [{"family": "Nirwan", "given": "Neha", "initials": "N"}, {"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Singh", "given": "Pratima", "initials": "P"}, {"family": "Bandyopadhyay", "given": "Sutirtha", "initials": "S"}, {"family": "Vinothkumar", "given": "Kutti R", "initials": "KR", "orcid": "0000-0002-6746-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bad216089a24c7f950de5a7f05939dc.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Saikrishnan", "given": "Kayarat", "initials": "K", "orcid": "0000-0003-4177-8508", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc61783f167447e2bd214c8ceb1e5074.json"}}], "type": "journal article", "published": "2019-07-11", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3058", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 \u00c5 structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the \u03b3 subunit complexed to \u03b1 3\u03b23 of F1-ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.", "doi": "10.1038/s41467-019-11084-1", "pmid": "31296862", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11084-1"}, {"db": "pmc", "key": "PMC6624300"}], "notes": "Cryo-EM maps and models are deposited in the Electron Microscopy and Protein Data Banks: EMD-0310 and 6HZ4. Maps and coordinates of five major classes are deposited \u2014 EMD-0311 and 6HZ5; EMD-0312 and 6HZ6; EMD-0313 and 6HZ7; EMD-0314 and 6HZ8; EMD-0315 and 6HZ9. Other data are available from the corresponding authors upon reasonable request.", "created": "2019-08-21T10:53:27.809Z", "modified": "2021-06-16T16:13:49.944Z"}]}