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Yorodumi- EMDB-2012: The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2012 | |||||||||
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Title | The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 | |||||||||
Map data | Structure of the M. thermautotrophicus 50S-aIF6 complex | |||||||||
Sample |
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Keywords | 50S ribosomal subunit / protein synthesis / initiation factor 6 | |||||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA / cytosolic ribosome / translation initiation factor activity / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome ...ribonuclease P activity / tRNA 5'-leader removal / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA / cytosolic ribosome / translation initiation factor activity / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / modification-dependent protein catabolic process / protein tag activity / large ribosomal subunit / ribosome biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / ubiquitin protein ligase binding / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 6.6 Å | |||||||||
Authors | Greber BJ / Boehringer D / Godinic-Mikulcic V / Crnkovic A / Ibba M / Weygand-Durasevic I / Ban N | |||||||||
Citation | Journal: J Mol Biol / Year: 2012 Title: Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. Authors: Basil J Greber / Daniel Boehringer / Vlatka Godinic-Mikulcic / Ana Crnkovic / Michael Ibba / Ivana Weygand-Durasevic / Nenad Ban / Abstract: Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains ...Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2012.map.gz | 19.5 MB | EMDB map data format | |
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Header (meta data) | emd-2012-v30.xml emd-2012.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | EMD2012_image_for_emdb.jpg | 165.1 KB | ||
Masks | emd_2012_msk_1.map | 22.2 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2012 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2012 | HTTPS FTP |
-Validation report
Summary document | emd_2012_validation.pdf.gz | 290.8 KB | Display | EMDB validaton report |
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Full document | emd_2012_full_validation.pdf.gz | 289.9 KB | Display | |
Data in XML | emd_2012_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2012 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2012 | HTTPS FTP |
-Related structure data
Related structure data | 4adxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2012.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the M. thermautotrophicus 50S-aIF6 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: NONE
Annotation | NONE | ||||||||||||
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File | emd_2012_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 50S ribosomal subunit in complex with archaeal initiation factor 6
Entire | Name: 50S ribosomal subunit in complex with archaeal initiation factor 6 |
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Components |
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-Supramolecule #1000: 50S ribosomal subunit in complex with archaeal initiation factor 6
Supramolecule | Name: 50S ribosomal subunit in complex with archaeal initiation factor 6 type: sample / ID: 1000 / Details: none / Oligomeric state: Equimolar complex of 50S and aIF6 / Number unique components: 2 |
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Molecular weight | Theoretical: 1.6 MDa |
-Supramolecule #1: Methanothermobacter thermautotrophicus 50S ribosomal subunit
Supramolecule | Name: Methanothermobacter thermautotrophicus 50S ribosomal subunit type: complex / ID: 1 / Name.synonym: Large ribosomal subunit / Recombinant expression: No Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S |
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Source (natural) | Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea) Location in cell: Cytoplasm |
Molecular weight | Theoretical: 1.6 MDa |
-Macromolecule #1: aIF6
Macromolecule | Name: aIF6 / type: protein_or_peptide / ID: 1 / Name.synonym: archaeal initiation factor 6 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea) Location in cell: Cytoplasm |
Molecular weight | Theoretical: 23 KDa |
Sequence | UniProtKB: Translation initiation factor 6 / InterPro: Translation initiation factor IF6 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 20 mM Tris-HCl pH 8, 20 mM MgCl2, 50 mM NH4Cl |
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Staining | Type: NEGATIVE / Details: cryo |
Grid | Details: Quantifoil holey carbon grid R2/1 |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: manual blotting |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Average: 87 K |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 83000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: per frame |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic-5, SPIDER / Number images used: 70364 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation |
Output model | PDB-4adx: |
-Atomic model buiding 2
Initial model | PDB ID: 3o58 |
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Software | Name: Chimera |
Details | Protocol: rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation |
Output model | PDB-4adx: |
-Atomic model buiding 3
Initial model | PDB ID: 4a17 |
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Software | Name: Chimera |
Details | Protocol: rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation |
Output model | PDB-4adx: |