4CXH

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


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: https://doi.org/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 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; Max-Planck Institut für Molekulare Genetik, Abteilung Vingron, AG Ribosomen, 14195 Berlin, Ihnestraße 73, Germany; Institute of Molecular Biology and Genetics, Group of Protein Biosynthesis, 03143 Kiev, Ukraine.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR 1AC [auth A]437Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q9YAV0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YAV0 
Go to UniProtKB:  Q9YAV0
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UniProt GroupQ9YAV0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US12D [auth X]143Oryctolagus cuniculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62266 (Homo sapiens)
Explore P62266 
Go to UniProtKB:  P62266
PHAROS:  P62266
GTEx:  ENSG00000186468 
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UniProt GroupP62266
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S RRNA - H44A [auth 1]135Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S RRNA - H89B [auth 2]50Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
TRANSFER RNAE [auth Y]76Oryctolagus cuniculus
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Entity ID: 6
MoleculeChains LengthOrganismImage
18S RRNA - H5-H14F [auth a]48Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
18S RRNA - H8G [auth b]17Oryctolagus cuniculus
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Entity ID: 8
MoleculeChains LengthOrganismImage
28S RRNA - H95H [auth c]19Oryctolagus cuniculus
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Entity ID: 9
MoleculeChains LengthOrganismImage
MESSENGER RNAI [auth x]28Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download Ideal Coordinates CCD File 
J [auth Y]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Revision History  (Full details and data files)

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