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Structure paper

TitleEvolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.
Journal, issue, pagesScience, Vol. 362, Issue 6413, Year 2018
Publish dateOct 26, 2018
AuthorsDavid J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban
External linksPubMed:30213880 / Publisher's page
KeywordsRIBOSOME / mitoribosome / translation / Trypanosoma / small ribosomal subunit / 9S rRNA / ribosomal protein / mitochondrial initiation factor IF-3 / large ribosomal subunit / 12S rRNA
MethodsEM (single particle)
Resolution3.08 - 7.8 A
Structure data

PDB-6hiw:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete small mitoribosomal subunit in complex with mt-IF-3

PDB-6hix:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the large mitoribosomal subunit

PDB-6hiy:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3

PDB-6hiz:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit

EMDB-0230:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete small mitoribosomal subunit in complex with mt-IF-3

EMDB-0231:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the large mitoribosomal subunit

EMDB-0232:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3

EMDB-0233:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit

EMDB-0229:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete mitoribosome

PDB-6hiv:
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete mitoribosome

Chemicals

ChemComp-ZN:
ZINC IONZinc

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATEUridine triphosphate

ChemComp-MG:
MAGNESIUM IONMagnesium

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

ChemComp-SPD:
SPERMIDINESpermidine

ChemComp-SPM:
SPERMINESpermine

ChemComp-HOH:
WATERWater

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDENicotinamide adenine dinucleotide

ChemComp-SER:
SERINESerine

Source
  • trypanosoma brucei brucei (eukaryote)
  • Trypanosoma brucei brucei (eukaryote)

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Feb 20, 2018. PDBj/BINDS workshop in Osaka University

PDBj/BINDS workshop in Osaka University

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    Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
    • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
    • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

    External links: The 2017 Nobel Prize in Chemistry - Press Release

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    Jul 12, 2017. Major update of PDB

    Major update of PDB

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    • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

    External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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    EMN Papers

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