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- PDB-4v6u: Promiscuous behavior of proteins in archaeal ribosomes revealed b... -
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Basic information
Entry | Database: PDB / ID: 4v6u | |||||||||
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Title | Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes | |||||||||
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![]() | RIBOSOME / archaea / archaeal / ribosomal / 70S / kink-turn / protein synthesis / RNA | |||||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / rRNA processing / large ribosomal subunit / ribosome biogenesis ...ribonuclease P activity / tRNA 5'-leader removal / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / rRNA processing / large ribosomal subunit / ribosome biogenesis / regulation of translation / 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 / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
![]() | Armache, J.-P. / Anger, A.M. / Marquez, V. / Frankenberg, S. / Froehlich, T. / Villa, E. / Berninghausen, O. / Thomm, M. / Arnold, G.J. / Beckmann, R. / Wilson, D.N. | |||||||||
![]() | ![]() Title: Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution. Authors: Jean-Paul Armache / Andreas M Anger / Viter Márquez / Sibylle Franckenberg / Thomas Fröhlich / Elizabeth Villa / Otto Berninghausen / Michael Thomm / Georg J Arnold / Roland Beckmann / Daniel N Wilson / ![]() Abstract: In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, ...In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, only molecular models of large 50S subunits have been reported for archaea. Here, we present a complete molecular model for the Pyrococcus furiosus 70S ribosome based on a 6.6 Å cryo-electron microscopy map. Moreover, we have determined cryo-electron microscopy reconstructions of the Euryarchaeota Methanococcus igneus and Thermococcus kodakaraensis 70S ribosomes and Crenarchaeota Staphylothermus marinus 50S subunit. Examination of these structures reveals a surprising promiscuous behavior of archaeal ribosomal proteins: We observe intersubunit promiscuity of S24e and L8e (L7ae), the latter binding to the head of the small subunit, analogous to S12e in eukaryotes. Moreover, L8e and L14e exhibit intrasubunit promiscuity, being present in two copies per archaeal 50S subunit, with the additional binding site of L14e analogous to the related eukaryotic r-protein L27e. Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 506.2 KB | Display | |
Data in CIF | ![]() | 769.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2009M ![]() 2170C ![]() 2171C ![]() 2172C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
+30S ribosomal protein ... , 24 types, 25 molecules AQAKAIAGAWACABARADANAXAMAEAJAOAFASAYATAAAHAPAVB6AL
-Protein , 3 types, 3 molecules A9AUBk
#9: Protein | Mass: 4868.993 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#30: Protein | Mass: 17394.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 37166.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 5 types, 5 molecules A1A2A0B1B3
#11: RNA chain | Mass: 24880.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#21: RNA chain | Mass: 485455.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: RNA chain | Mass: 24538.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#67: RNA chain | Mass: 990820.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#68: RNA chain | Mass: 40689.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 36 types, 39 molecules A3BGB4BYBOBCB5BKBLBfBUBbBeBEBaBTBWBiBABIBRBQBVBjBBBDBFBhBHBZ...
-Details
Sequence details | THE SEQUENCE OF 30S RIBOSOMAL PROTEIN SX IS NOT KNOWN. |
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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 |
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Sample preparation
Component | Name: Pyrococcus furiosus 70S ribosome / Type: RIBOSOME |
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Buffer solution | Name: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP pH: 8.2 Details: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil grids (3/3) with 2 nm carbon on top |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % Details: Blot for 10 seconds before plunging into liquid ethane, using 2 layers of filter paper (FEI VITROBOT) |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: Wiener Filter | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: Single Particle / Resolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 10000 / Nominal pixel size: 1.24 Å / Actual pixel size: 1.24 Å Details: sorting for ribosome conformation and ligand presence was performed Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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