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	Capturing eukaryotic ribosome dynamics in situ at high resolution.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 32, Issue 4, Page 698-708, Year 2025
Publish date	Jan 9, 2025
Authors	Jing Cheng / Chunling Wu / Junxi Li / Qi Yang / Mingjie Zhao / Xinzheng Zhang /
PubMed Abstract	Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ...Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.
External links	Nat Struct Mol Biol / PubMed:39789210
Methods	EM (single particle)
Resolution	3.2 - 4.7 Å
Structure data	EMDB-38654: State 8a (S8a) of yeast 80S ribosome bound to 3 tRNAs and eEF1A and eEF3 during mRNA decoding Method: EM (single particle) / Resolution: 3.8 Å EMDB-38655: State 8 (S8) of yeast 80S ribosome bound to 3 tRNAs and eEF1A during mRNA decoding Method: EM (single particle) / Resolution: 3.5 Å 38656 8z70 EMDB-38656: State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs and eEF1A during mRNA decoding PDB-8z70: State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Method: EM (single particle) / Resolution: 3.2 Å 38657 8z71 EMDB-38657, PDB-8z71: State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Method: EM (single particle) / Resolution: 3.6 Å EMDB-38658: State 2a (S2a) of yeast 80S ribosome bound to 2 tRNAs during peptidyl transfer Method: EM (single particle) / Resolution: 3.7 Å EMDB-38659: State 2b (S2b) of yeast 80S ribosome bound to 2 tRNAs during peptidyl transfer Method: EM (single particle) / Resolution: 3.3 Å 38660 8xu8 EMDB-38660, PDB-8xu8: State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Method: EM (single particle) / Resolution: 3.4 Å EMDB-38661: State 2d (S2d) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transfer Method: EM (single particle) / Resolution: 3.5 Å EMDB-38662: State 2e (S2e) of yeast 80S ribosome bound to 2 tRNAs during peptidyl transfer Method: EM (single particle) / Resolution: 4.2 Å EMDB-38663: State 2f (S2f) of yeast 80S ribosome bound to 2 tRNAs during peptidyl transfer Method: EM (single particle) / Resolution: 3.9 Å EMDB-38664: State 3 (S3) of yeast 80S ribosome bound to 2 tRNAs during translocation Method: EM (single particle) / Resolution: 4.0 Å EMDB-38665: State 4 (S4) of yeast 80S ribosome bound to 2 tRNAs and eEF2 during translocation Method: EM (single particle) / Resolution: 3.7 Å 38666 8yld EMDB-38666, PDB-8yld: State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Method: EM (single particle) / Resolution: 3.9 Å EMDB-38667: State 5 (S5) of yeast 80S ribosome bound to 2 tRNAs and eEF2 during translocation Method: EM (single particle) / Resolution: 3.8 Å 38668 8ylr EMDB-38668, PDB-8ylr: State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Method: EM (single particle) / Resolution: 3.9 Å EMDB-38669: State 7 (S7) of yeast 80S ribosome bound to 2 tRNAs and eEF2 during tranlocation Method: EM (single particle) / Resolution: 3.7 Å EMDB-38670: State 9 (S9) of yeast 80S ribosome bound to 2 tRNAs Method: EM (single particle) / Resolution: 4.7 Å EMDB-38671: State 10 (S10) of yeast 80S ribosome bound to A tRNA Method: EM (single particle) / Resolution: 4.7 Å
Source	saccharomyces cerevisiae s288c (yeast) oryctolagus cuniculus (rabbit)
Keywords	TRANSLATION / 80S / compact eEF2 / elongation cycle / rotated / RIBOSOME / eEF3 / eEF2