4CXG

Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement.

Budkevich, T.V.Giesebrecht, J.Behrmann, E.Loerke, J.Ramrath, D.J.Mielke, T.Ismer, J.Hildebrand, P.W.Tung, C.S.Nierhaus, K.H.Sanbonmatsu, K.Y.Spahn, C.M.

(2014) Cell 158: 121

  • DOI: 10.1016/j.cell.2014.04.044
  • Primary Citation of Related Structures:  
    4CXG, 4CXH, 4UJE

  • PubMed Abstract: 
  • The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosom ...

    The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: christian.spahn@charite.de.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR 1AA437Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q9YAV0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
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Go to UniProtKB:  Q9YAV0
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US12X143Oryctolagus cuniculusMutation(s): 0 
Find proteins for P62266 (Homo sapiens)
Explore P62266 
Go to UniProtKB:  P62266
NIH Common Fund Data Resources
PHAROS  P62266
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S RRNA - H441135Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
28S RRNA - H89250Oryctolagus cuniculus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
TRANSFER RNAY76Oryctolagus cuniculus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
18S RRNA - H5-H14a48Oryctolagus cuniculus
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  • Entity ID: 7
    MoleculeChainsLengthOrganismImage
    18S RRNA - H8b17Oryctolagus cuniculus
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    • Entity ID: 8
      MoleculeChainsLengthOrganismImage
      28S RRNA - H95c19Oryctolagus cuniculus
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      Entity ID: 9
      MoleculeChainsLengthOrganismImage
      MESSENGER RNAx28Escherichia coli
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PHE
      Query on PHE

      Download CCD File 
      Y
      PHENYLALANINE
      C9 H11 N O2
      COLNVLDHVKWLRT-QMMMGPOBSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 8.70 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2014-07-16
        Type: Initial release
      • Version 2.0: 2017-08-23
        Changes: Atomic model, Data collection, Derived calculations, Refinement description
      • Version 3.0: 2019-06-26
        Changes: Data collection, Derived calculations, Non-polymer description, Structure summary