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- PDB-3j0p: Core of mammalian 80S pre-ribosome in complex with tRNAs fitted t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3j0p | ||||||
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Title | Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 1 | ||||||
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![]() | RIBOSOME / Mammalia / translation / elongation cycle / tRNA | ||||||
Function / homology | ![]() SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome ...SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 Å | ||||||
![]() | Budkevich, T. / Giesebrecht, J. / Altman, R. / Munro, J. / Mielke, T. / Nierhaus, K. / Blanchard, S. / Spahn, C.M. | ||||||
![]() | ![]() Title: Structure and dynamics of the mammalian ribosomal pretranslocation complex. Authors: Tatyana Budkevich / Jan Giesebrecht / Roger B Altman / James B Munro / Thorsten Mielke / Knud H Nierhaus / Scott C Blanchard / Christian M T Spahn / ![]() Abstract: Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to ...Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to which these differences influence the molecular mechanism of translation remains elusive. Multiparticle cryo-electron microscopy and single-molecule FRET investigations of the mammalian pretranslocation complex reveal spontaneous, large-scale conformational changes, including an intersubunit rotation of the ribosomal subunits. Through structurally related processes, tRNA substrates oscillate between classical and at least two distinct hybrid configurations facilitated by localized changes in their L-shaped fold. Hybrid states are favored within the mammalian complex. However, classical tRNA positions can be restored by tRNA binding to the E site or by the eukaryotic-specific antibiotic and translocation inhibitor cycloheximide. These findings reveal critical distinctions in the structural and energetic features of bacterial and mammalian ribosomes, providing a mechanistic basis for divergent translation regulation strategies and species-specific antibiotic action. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 386 KB | Display | ![]() |
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PDB format | ![]() | 301.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5328MC ![]() 5326C ![]() 5327C ![]() 5329C ![]() 3j0lC ![]() 3j0oC ![]() 3j0qC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-40S ribosomal RNA ... , 7 types, 7 molecules acdgGfh
#1: RNA chain | Mass: 15500.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 5426.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 2283.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: RNA chain | Mass: 9934.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: RNA chain | Mass: 4132.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: RNA chain | Mass: 6794.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: RNA chain | Mass: 35735.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Ribosomal protein ... , 4 types, 4 molecules SLXB
#8: Protein | Mass: 14027.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 15646.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 7893.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 24014.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-60S ribosomal RNA ... , 3 types, 3 molecules 237
#11: RNA chain | Mass: 36097.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: RNA chain | Mass: 3859.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: RNA chain | Mass: 15929.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 4 types, 4 molecules YyWw
#15: RNA chain | Mass: 24156.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#16: RNA chain | Mass: 872.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: RNA chain | Mass: 613.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Details
Sequence details | ENTRY HAS BEEN MODELED WITH 60S RIBOSOMAL RNA AND PROTEINS FROM SACCHAROMYCES CEREVISIAE, 40S ...ENTRY HAS BEEN MODELED WITH 60S RIBOSOMAL RNA AND PROTEINS FROM SACCHAROMY |
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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: Mammalian 80S-PRE complex in rotated 1 state / Type: RIBOSOME |
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Buffer solution | Name: polyamine buffer / pH: 7.5 / Details: polyamine buffer |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Carbon coated Quantifoil grids |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: Ethane / Vitrobot (FEI) flash-frozen in liquid ethane |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Oct 17, 2006 / Details: LOW DOSE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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 |
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CTF correction | Details: CTF CORRECTION OF EACH DEFOCUS GROUP VOLUME PRIOR TO BACK PROJECTION | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Method: SINGLE PARTICLE / Resolution: 10.6 Å / Num. of particles: 22212 / Nominal pixel size: 2.52 Å / Actual pixel size: 2.52 Å / Details: PROJECTION MATCHING / Symmetry type: POINT | |||||||||||||||
Atomic model building |
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Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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