8B6Z

CryoEM Structure of Extended eEF1A bound to the Ribosome in the Classical Pre State

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-09-27 Released: 2022-12-07 
  • Deposition Author(s): Gemmer, M., Fedry, J.M.M., Forster, F.G.
  • Funding Organization(s): European Research Council (ERC), Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Visualization of translation and protein biogenesis at the ER membrane.

Gemmer, M.Chaillet, M.L.van Loenhout, J.Cuevas Arenas, R.Vismpas, D.Grollers-Mulderij, M.Koh, F.A.Albanese, P.Scheltema, R.A.Howes, S.C.Kotecha, A.Fedry, J.Forster, F.

(2023) Nature 614: 160-167

  • DOI: https://doi.org/10.1038/s41586-022-05638-5
  • Primary Citation of Related Structures:  
    8B6L, 8B6Z

  • PubMed Abstract: 

    The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome 1,2 . It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation 3-7 , insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery.


  • Organizational Affiliation

    Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 1-alpha 2463Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q05639 (Homo sapiens)
Explore Q05639 
Go to UniProtKB:  Q05639
PHAROS:  Q05639
GTEx:  ENSG00000101210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05639
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
28S ribosomal RNA5,070Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union724425
Netherlands Organisation for Scientific Research (NWO)Netherlands724.016.001
Netherlands Organisation for Scientific Research (NWO)Netherlands212.152

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references