3J0Q

Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and dynamics of the Mammalian ribosomal pretranslocation complex.

Budkevich, T.Giesebrecht, J.Altman, R.B.Munro, J.B.Mielke, T.Nierhaus, K.H.Blanchard, S.C.Spahn, C.M.

(2011) Mol Cell 44: 214-224

  • DOI: 10.1016/j.molcel.2011.07.040
  • Primary Citation of Related Structures:  
    3J0Q, 3J0L, 3J0O, 3J0P

  • PubMed 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 which these differences influence the molecular mechanism of translation remains elusive ...

    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.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.



Macromolecules

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15S125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S23L141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S30X68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L10aB213Oryctolagus cuniculusMutation(s): 0 
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P0CX43
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L10J219Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11k165Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q3E757
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
40S ribosomal RNA fragmenta48Oryctolagus cuniculus
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  • Entity ID: 2
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    40S ribosomal RNA fragmentc17Oryctolagus cuniculus
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    • Entity ID: 3
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      40S ribosomal RNA fragmentd7Oryctolagus cuniculus
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      Entity ID: 4
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      40S ribosomal RNA fragmentg31Oryctolagus cuniculus
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      • Entity ID: 5
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        40S ribosomal RNA fragmentG13Oryctolagus cuniculus
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        Entity ID: 6
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        40S ribosomal RNA fragmentf21Oryctolagus cuniculus
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        Entity ID: 7
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        40S ribosomal RNA fragmenth111Oryctolagus cuniculus
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        Entity ID: 11
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        60S ribosomal RNA fragment2112Oryctolagus cuniculus
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        • Entity ID: 12
          MoleculeChainsLengthOrganismImage
          60S ribosomal RNA fragment312Oryctolagus cuniculus
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          • Entity ID: 13
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            60S ribosomal RNA fragment919Oryctolagus cuniculus
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            Entity ID: 14
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            60S ribosomal RNA fragment750Oryctolagus cuniculus
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            Entity ID: 18
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            tRNAW, Y77Oryctolagus cuniculus
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            • Entity ID: 19
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              mRNA fragmenty3Oryctolagus cuniculus
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              • Entity ID: 20
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                mRNA fragmentw2Oryctolagus cuniculus
                Experimental Data & Validation

                Experimental Data

                • Method: ELECTRON MICROSCOPY
                • Resolution: 10.6 Å
                • Aggregation State: PARTICLE 
                • Reconstruction Method: SINGLE PARTICLE 

                Structure Validation

                View Full Validation Report



                Entry History 

                Deposition Data

                Revision History 

                • Version 1.0: 2011-11-16
                  Type: Initial release
                • Version 1.1: 2018-07-18
                  Changes: Data collection, Database references