3J0O

Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9A cryo-EM map: classic PRE state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 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
  • Structures With Same Primary Citation

  • 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: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S5T192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S14K140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S23L141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S30X68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15S125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10aB213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L36aF95Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmenta48Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentb12Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentc17Oryctolagus cuniculus
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Entity ID: 4
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentd7Oryctolagus cuniculus
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Entity ID: 5
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmente4Oryctolagus cuniculus
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Entity ID: 6
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentE5Oryctolagus cuniculus

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Entity ID: 7
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentf21Oryctolagus cuniculus

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Entity ID: 8
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentg31Oryctolagus cuniculus
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Entity ID: 9
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmentG13Oryctolagus cuniculus

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Entity ID: 10
MoleculeChainsLengthOrganism
40S ribosomal RNA fragmenth111Oryctolagus cuniculus

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Entity ID: 16
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment2112Oryctolagus cuniculus
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Entity ID: 17
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment312Oryctolagus cuniculus
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Entity ID: 18
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment414Oryctolagus cuniculus
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Entity ID: 19
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment56Oryctolagus cuniculus
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Entity ID: 20
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment619Oryctolagus cuniculus

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Entity ID: 21
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment750Oryctolagus cuniculus
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Entity ID: 22
MoleculeChainsLengthOrganism
60S ribosomal RNA fragment820Oryctolagus cuniculus

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Entity ID: 25
MoleculeChainsLengthOrganism
tRNAV, W, Y76Oryctolagus cuniculus
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Entity ID: 26
MoleculeChainsLengthOrganism
mRNA fragmentv, y3Oryctolagus cuniculus
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Entity ID: 27
MoleculeChainsLengthOrganism
mRNA fragmentw2Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

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