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Yorodumi- PDB-4v4b: Structure of the ribosomal 80S-eEF2-sordarin complex from yeast o... -
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-Basic information
Entry | Database: PDB / ID: 4v4b | |||||||||
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Title | Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. | |||||||||
Components |
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Keywords | RIBOSOME / 80S ribosome / 40S ribosomal subunit / eEF2 / tRNA translocation / sordarin / cryo-EM | |||||||||
Function / homology | Function and homology information : / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / Protein hydroxylation / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex ...: / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / Protein hydroxylation / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Neutrophil degranulation / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / protein-folding chaperone binding / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å | |||||||||
Authors | Spahn, C.M. / Gomez-Lorenzo, M.G. / Grassucci, R.A. / Jorgensen, R. / Andersen, G.R. / Beckmann, R. / Penczek, P.A. / Ballesta, J.P.G. / Frank, J. | |||||||||
Citation | Journal: EMBO J / Year: 2004 Title: Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. Authors: Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank / Abstract: An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and ...An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction. #1: Journal: Nat Struct Biol / Year: 1999 Title: EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Authors: R K Agrawal / A B Heagle / P Penczek / R A Grassucci / J Frank / Abstract: Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the ...Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the pretranslocational complex and for the completion of translocation. In addition, large conformational changes have been identified in the ribosome. The head of the 30S subunit shifts toward the L1 protein side, and the L7/L12 stalk becomes bifurcated upon EF-G binding. Upon GTP hydrolysis, the bifurcation is reversed and an arc-like connection is formed between the base of the stalk and EF-G. #2: Journal: PROG.NUCLEIC ACID RES.MOL.BIOL. / Year: 1996 Title: The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery. Authors: Ballesta, J.P. / Remacha, M. #3: Journal: Science / Year: 2000 Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. | |||||||||
History |
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Remark 400 | COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE ...COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE 80S RIBOSOME. THIS FILE, 1S1H, CONTAINS THE 40S SUBUNIT. THE 60S RIBOSOMAL SUBUNIT IS IN FILE 1S1I. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v4b.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v4b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4v4b_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 4v4b_validation.xml.gz | 686.4 KB | Display | |
Data in CIF | 4v4b_validation.cif.gz | 939.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4b ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4b | HTTPS FTP |
-Related structure data
Related structure data | 1067MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-RNA chain , 3 types, 3 molecules AAB3B4
#1: RNA chain | Mass: 489331.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: modelled as analogous molecule of T. thermophilus taken from PDB entry 1FJF Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 155076 |
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#18: RNA chain | Mass: 971012.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK AND SUPPLEMENTED WITH SEQUENCES FROM PDB ENTRIES 1MMS, 1MZP AND 1GIY Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 3377778 |
#19: RNA chain | Mass: 40298.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 3377779 |
-Protein , 1 types, 1 molecules AT
#2: Protein | Mass: 93407.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324 |
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-40S ribosomal protein ... , 15 types, 15 molecules ABACADAEAGAHAIAJAKALAMANAOAQAS
#3: Protein | Mass: 20355.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905 |
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#4: Protein | Mass: 21321.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750 |
#5: Protein | Mass: 20363.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516 |
#6: Protein | Mass: 15639.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443 |
#7: Protein | Mass: 16577.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783 |
#8: Protein | Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04648, UniProt: Q3E7Y3*PLUS |
#9: Protein | Mass: 15746.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS |
#10: Protein | Mass: 11352.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701 |
#11: Protein | Mass: 14459.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367 |
#12: Protein | Mass: 12879.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32827, UniProt: P0CX30*PLUS |
#13: Protein | Mass: 15485.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS |
#14: Protein/peptide | Mass: 4328.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41058 |
#15: Protein | Mass: 7841.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756 |
#16: Protein | Mass: 8777.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS |
#17: Protein | Mass: 8901.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855 |
+60S ribosomal protein ... , 28 types, 28 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVB0BWBXBYBZB9
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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