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Yorodumi- PDB-4v8m: High-resolution cryo-electron microscopy structure of the Trypano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8m | |||||||||||||||
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Title | High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome | |||||||||||||||
Components |
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Keywords | RIBOSOME / EUKARYOTIC / KINETOPLASTIDS / EXPANSION SEGMENTS | |||||||||||||||
Function / homology | Function and homology information organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal large subunit assembly / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / protein kinase C binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / regulation of cell population proliferation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) TRYPANOSOMA BRUCEI (eukaryote) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.57 Å | |||||||||||||||
Authors | Hashem, Y. / des Georges, A. / Fu, J. / Buss, S.N. / Jossinet, F. / Jobe, A. / Zhang, Q. / Liao, H.Y. / Grassucci, R.A. / Bajaj, C. ...Hashem, Y. / des Georges, A. / Fu, J. / Buss, S.N. / Jossinet, F. / Jobe, A. / Zhang, Q. / Liao, H.Y. / Grassucci, R.A. / Bajaj, C. / Westhof, E. / Madison-Antenucci, S. / Frank, J. | |||||||||||||||
Citation | Journal: Nature / Year: 2013 Title: High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Authors: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison- ...Authors: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison-Antenucci / Joachim Frank / Abstract: Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and ...Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs. | |||||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "5B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "5B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "SA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v8m.cif.gz | 5.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8m_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4v8m_full_validation.pdf.gz | 7.7 MB | Display | |
Data in XML | 4v8m_validation.xml.gz | 930.3 KB | Display | |
Data in CIF | 4v8m_validation.cif.gz | 1.3 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8m ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8m | HTTPS FTP |
-Related structure data
Related structure data | 2239MC 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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1 |
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-Components
+40S RIBOSOMAL PROTEIN ... , 25 types, 25 molecules A0A1A2A3A5A6ACADAFAGAHAIAJAKALAMAPARASATAUAWAXAYAZ
-RIBOSOMAL PROTEIN ... , 9 types, 9 molecules A4A8AOAQAVBQBfBmBn
#5: Protein | Mass: 23889.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q38FD9 |
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#9: Protein | Mass: 6679.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 |
#22: Protein | Mass: 18891.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q583K7 |
#24: Protein | Mass: 13248.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 |
#29: Protein | Mass: 12837.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q384J9 |
#50: Protein | Mass: 26461.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q38CY7 |
#65: Protein | Mass: 48802.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q581Q1 |
#72: Protein | Mass: 12491.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q38CY6 |
#73: Protein | Mass: 10128.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q386L1 |
-Protein , 7 types, 7 molecules A7A9AEBJBPBhBs
#8: Protein | Mass: 34727.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q383E1 |
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#10: Protein | Mass: 16936.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q57WI3 |
#13: Protein | Mass: 20132.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q38CI4 |
#43: Protein | Mass: 24640.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q383V8 |
#49: Protein | Mass: 21742.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: P55842 |
#67: Protein | Mass: 21752.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: Q38DH8 |
#78: Protein | Mass: 14685.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / References: UniProt: P21899 |
-RNA chain , 10 types, 10 molecules BABBBCBDBEBFBGBHAAAB
#34: RNA chain | Mass: 595796.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) / References: GenBank: X14553 |
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#35: RNA chain | Mass: 471450.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) / References: GenBank: X14553 |
#36: RNA chain | Mass: 54224.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#37: RNA chain | Mass: 38316.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#38: RNA chain | Mass: 67234.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#39: RNA chain | Mass: 23079.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#40: RNA chain | Mass: 58889.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#41: RNA chain | Mass: 43388.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
#85: RNA chain | Mass: 724377.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) / References: GenBank: M12676 |
#86: RNA chain | Mass: 23545.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI (eukaryote) |
+60S RIBOSOMAL PROTEIN ... , 35 types, 35 molecules BIBKBLBMBNBOBRBSBTBUBVBWBXBYBZBaBbBcBdBeBgBiBjBkBlBoBpBqBrBt...
-Details
Sequence details | CHAINS 8 AND Q ARE MODELLED USING T. CRUZI SEQUENCE UNP ACCESSIONS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRYPANOSOMA BRUCEI 80S RIBOSOME / Type: RIBOSOME / Details: MICROGRAPHS SELECTED VISUALLY AFTER SCANNING |
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Buffer solution | Name: 20 MM HEPES, 10MM MGCL2, 500 MM KCL AND 5 MM BETA-ME / pH: 7.2 Details: 20 MM HEPES, 10MM MGCL2, 500 MM KCL AND 5 MM BETA-ME |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHAN |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jan 1, 2011 Details: MICROGRAPHS SCANNED WITH NIKON SUPER COOLSCAN 9000ED |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm |
Specimen holder | Temperature: 93.15 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 1102 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: PHASE-FLIPPING | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: REFERENCE BASED RECONSTRUCTION METHOD / Resolution: 5.57 Å / Num. of particles: 164000 / Nominal pixel size: 1.09 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2239 (DEPOSITION ID: 11259). THE STRUCTURE OF THE 80S FROM YEAST (3U5B AND OTHERS) AS WELL AS THE STRUCTURE OF THE 60S FROM TETRAHYMENA ...Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2239 (DEPOSITION ID: 11259). THE STRUCTURE OF THE 80S FROM YEAST (3U5B AND OTHERS) AS WELL AS THE STRUCTURE OF THE 60S FROM TETRAHYMENA THERMOPHILA (4A17 AND OTHERS) WERE USED AS STARTING MODEL FOR THE 60S SUBUNIT MODEL. THE 40S FROM TETRAHYMENA THERMOPHILA (2XZM AND 2XZN) AS WELL AS THE 80S FROM YEAST WERE USED AS STARTING MODEL FOR THE 40S SUBUNIT MODEL. THE 80S MODEL OF TRITICUM AESTIVUM (3IZR AND OTHERS) WAS USED TO FIT MISSING PROTEINS FORM THE TWO X-RAY STRUCTURES. Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 5.57 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.57 Å
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