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Structure paper

TitleAnalysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 5187, Year 2020
Publish dateOct 14, 2020
AuthorsYuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts /
PubMed AbstractMitoribosomes 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 ...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 (IF) 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.
External linksNat Commun / PubMed:33056988 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.5 Å
Structure data

EMDB-10958, PDB-6yw5:
The structure of the small subunit of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 2.85 Å

EMDB-10961:
Cryo-EM map of the head of the small subunit of the mitoribosome from Neurospora crassa.
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-10962:
Cryo-EM map of the body of the small subunit of the mitoribosome from Neurospora crassa.
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-10963:
Cryo-EM map of the tail of the small subunit of the mitoribosome from Neurospora crassa.
Method: EM (single particle) / Resolution: 2.86 Å

EMDB-10965, PDB-6ywe:
The structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state
Method: EM (single particle) / Resolution: 2.99 Å

EMDB-10966:
Cryo-EM map of the core of the large subunit of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-10967:
Cryo-EM map of the L10 region of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-10968:
Cryo-EM map of the CP of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-10969:
Cryo-EM map of the head of the small subunit of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-10970:
Cryo-EM map of the body of the small subunit of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-10971:
Cryo-EM map of the L1 stalk region of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-10972:
Cryo-EM map of the tail region of the mitoribosome from Neurospora crassa with tRNA in the P/E state
Method: EM (single particle) / Resolution: 2.99 Å

EMDB-10973, PDB-6yws:
The structure of the large subunit of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 2.74 Å

EMDB-10974:
Cryo-EM map of the core of the large subunit of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-10975:
Cryo-EM map of the L10 region of the large subunit of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-10976:
Cryo-EM map of the CP of the large subunit of the mitoribosome from Neurospora crassa.
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-10977, PDB-6ywv:
The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-10978, PDB-6ywx:
The structure of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-10979:
Cryo-EM map of the core of the large subunit of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Method: EM (single particle) / Resolution: 2.99 Å

EMDB-10980:
Cryo-EM map of the L10 region of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-10981:
Cryo-EM map of the CP of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-10982:
Cryo-EM map of the head of the small subunit of the mitoribosome from Neurospora crassa
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-10983:
Cryo-EM map of the tail of the small subunit of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-10984:
Cryo-EM map of the body of the small subunit of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-10985, PDB-6ywy:
The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-10986:
Cryo-EM map of the core of the large subunit of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-10988:
Cryo-EM map of the L10 region of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-10989:
Cryo-EM map of the CP of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-10990:
Cryo-EM map of the head of the small subunit of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-10991:
Cryo-EM map of the body of the small subunit of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-10992:
Cryo-EM map for the tail of the small subunit of the mitoribosome from Neurospora crassa with tRNA bound to the P-site
Method: EM (single particle) / Resolution: 3.01 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-K:
Unknown entry

ChemComp-SPM:
SPERMINE

ChemComp-ZN:
Unknown entry

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

Source
  • neurospora crassa or74a (fungus)
  • neurospora crassa (fungus)
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108

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