Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
Journal, issue, pages	Elife, Vol. 5, Year 2016
Publish date	May 9, 2016
Authors	Priyanka D Abeyrathne / Cha San Koh / Timothy Grant / Nikolaus Grigorieff / Andrei A Korostelev /
PubMed Abstract	Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the ...Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.
External links	Elife / PubMed:27159452 / PubMed Central
Methods	EM (single particle)
Resolution	3.3 - 4.2 Å
Structure data	6643 5juo EMDB-6643: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5juo: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Method: EM (single particle) / Resolution: 4.0 Å 6644 5jup EMDB-6644: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jup: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Method: EM (single particle) / Resolution: 3.3 Å 6645 5jus EMDB-6645: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jus: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Method: EM (single particle) / Resolution: 4.2 Å 6646 5jut EMDB-6646: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jut: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Method: EM (single particle) / Resolution: 4.0 Å 6647 5juu EMDB-6647: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5juu: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Method: EM (single particle) / Resolution: 4.0 Å 6648 5juo EMDB-6648: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5juo: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Method: EM (single particle) / Resolution: 4.0 Å 6649 5jup EMDB-6649: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jup: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Method: EM (single particle) / Resolution: 3.6 Å 6650 5jus EMDB-6650: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jus: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Method: EM (single particle) / Resolution: 4.0 Å EMDB-6651: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome Method: EM (single particle) / Resolution: 4.2 Å 6652 5jut EMDB-6652: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5jut: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Method: EM (single particle) / Resolution: 3.9 Å 6653 5juu EMDB-6653: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome PDB-5juu: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Method: EM (single particle) / Resolution: 3.8 Å
Chemicals	ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-SO1*: [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
Source	saccharomyces cerevisiae (brewer's yeast) taura syndrome virus
Keywords	RIBOSOME / 80S-IRES / eEF2 / translocation / sordarin