3J0L

Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9.8A cryo-EM map: classic PRE state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.molcel.2011.07.040
  • Primary Citation of Related Structures:  
    3J0L, 3J0O, 3J0P, 3J0Q

  • 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5K [auth T]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14L [auth K]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23M [auth L]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S30N [auth X]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15O [auth S]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10aX [auth B]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10Y [auth J]219Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36aZ [auth F]95Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentA [auth a]48Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentB [auth b]12Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentC [auth c]17Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentD [auth d]7Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentE [auth e]4Oryctolagus cuniculus
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Entity ID: 6
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentF [auth E]5Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentG [auth f]21Oryctolagus cuniculus
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Entity ID: 8
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentH [auth g]31Oryctolagus cuniculus
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Entity ID: 9
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentI [auth G]13Oryctolagus cuniculus
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Entity ID: 10
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentJ [auth h]111Oryctolagus cuniculus
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Entity ID: 16
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentP [auth 1]50Oryctolagus cuniculus
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Entity ID: 17
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentQ [auth 2]112Oryctolagus cuniculus
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Entity ID: 18
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentR [auth 3]12Oryctolagus cuniculus
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Entity ID: 19
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentS [auth 4]14Oryctolagus cuniculus
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Entity ID: 20
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentT [auth 5]6Oryctolagus cuniculus
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Entity ID: 21
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentU [auth 6]19Oryctolagus cuniculus
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Entity ID: 22
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentV [auth 7]50Oryctolagus cuniculus
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Entity ID: 23
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentW [auth 8]20Oryctolagus cuniculus
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Entity ID: 27
MoleculeChains LengthOrganismImage
tRNAAA [auth Y],
CA [auth V],
EA [auth W]
76Oryctolagus cuniculus
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Entity ID: 28
MoleculeChains LengthOrganismImage
mRNA fragmentBA [auth y],
DA [auth v]
3Oryctolagus cuniculus
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Entity ID: 29
MoleculeChains LengthOrganismImage
mRNA fragmentFA [auth w]2Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Refinement description