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Yorodumi- PDB-4v7h: Structure of the 80S rRNA and proteins and P/E tRNA for eukaryoti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v7h | |||||||||
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Title | Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution | |||||||||
Components |
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Keywords | RIBOSOME / eukaryotic ribosome / 80S / RACK1 protein / flexible fitting | |||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | |||||||||
Biological species | Thermomyces lanuginosus (fungus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å | |||||||||
Authors | Taylor, D.J. / Devkota, B. / Huang, A.D. / Topf, M. / Narayanan, E. / Sali, A. / Harvey, S.C. / Frank, J. | |||||||||
Citation | Journal: Structure / Year: 2009 Title: Comprehensive molecular structure of the eukaryotic ribosome. Authors: Derek J Taylor / Batsal Devkota / Andrew D Huang / Maya Topf / Eswar Narayanan / Andrej Sali / Stephen C Harvey / Joachim Frank / Abstract: Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not ...Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v7h.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v7h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v7h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4v7h_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4v7h_validation.xml.gz | 345 KB | Display | |
Data in CIF | 4v7h_validation.cif.gz | 555.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7h ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7h | HTTPS FTP |
-Related structure data
Related structure data | 1345M M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules AAA7B3B4B5
#1: RNA chain | Mass: 567333.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
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#19: RNA chain | Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#51: RNA chain | Mass: 36339.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#52: RNA chain | Mass: 50369.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#53: RNA chain | Mass: 1024354.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
-40S ribosomal protein ... , 15 types, 15 molecules ABACADAEAGAHAIAJAKALAMANAOAQAS
#2: Protein | Mass: 21236.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
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#3: Protein | Mass: 20925.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#4: Protein | Mass: 18415.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#5: Protein | Mass: 17146.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#6: Protein | Mass: 20728.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#7: Protein | Mass: 14100.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#8: Protein | Mass: 15391.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#9: Protein | Mass: 10980.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#10: Protein | Mass: 13191.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#11: Protein | Mass: 12879.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#12: Protein | Mass: 15301.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#13: Protein/peptide | Mass: 5953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#14: Protein | Mass: 9842.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#15: Protein | Mass: 9133.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
#16: Protein | Mass: 7863.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
-Protein , 2 types, 2 molecules ARAT
#17: Protein | Mass: 34209.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
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#18: Protein | Mass: 15656.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) |
+60S ribosomal protein ... , 31 types, 31 molecules B0B1B2B8B9BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZ
-Details
Sequence details | THE RIBOSOME ORIGINATES FROM THERMOMYCES LANUGINOSUS HOWEVER THE MODEL WAS BUILT BASED ON THE ...THE RIBOSOME ORIGINATES |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY / Number of used crystals: 1 |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Thermomyces lanuginosus ribosome / Type: RIBOSOME |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: Apply sample, wait 30s, blot for 6s, plunge in liquid ethane |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jul 7, 2005 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1400 nm |
Specimen holder | Temperature: 84 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
Software | Name: OTHER / Classification: refinement | ||||||||||||
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EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 8.9 Å / Num. of particles: 102689 Details: SPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T LEU 79 are not properly linked. Distance ...Details: SPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T LEU 79 are not properly linked. Distance of C-N bond is 2.49 Angstrom. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation / Details: METHOD--Flexible fitting | ||||||||||||
Refinement | Highest resolution: 8.9 Å / Occupancy max: 1 / Occupancy min: 0 | ||||||||||||
Displacement parameters | Biso max: 362.94 Å2 / Biso mean: 4.424 Å2 / Biso min: 0 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.9 Å
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