3J0P

Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.6 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15H [auth S]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23I [auth L]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S30J [auth X]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10aN [auth B]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX43 
Go to UniProtKB:  P0CX43
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UniProt GroupP0CX43
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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 c]17Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentC [auth d]7Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentD [auth g]31Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentE [auth G]13Oryctolagus cuniculus
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Entity ID: 6
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentF [auth f]21Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
40S ribosomal RNA fragmentG [auth h]111Oryctolagus cuniculus
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Entity ID: 11
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentK [auth 2]112Oryctolagus cuniculus
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Entity ID: 12
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentL [auth 3]12Oryctolagus cuniculus
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Entity ID: 13
MoleculeChains LengthOrganismImage
60S ribosomal RNA fragmentM [auth 7]50Oryctolagus cuniculus
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Entity ID: 15
MoleculeChains LengthOrganismImage
tRNAO [auth Y]75Oryctolagus cuniculus
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Entity ID: 16
MoleculeChains LengthOrganismImage
mRNA fragmentP [auth y]3Oryctolagus cuniculus
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Entity ID: 17
MoleculeChains LengthOrganismImage
tRNAQ [auth W]77Oryctolagus cuniculus
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Entity ID: 18
MoleculeChains LengthOrganismImage
mRNA fragmentR [auth w]2Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.6 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, Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Refinement description