8B6L

Subtomogram average of the human Sec61-TRAP-OSTA-translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1476Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P61619
GTEx:  ENSG00000058262 
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UniProt GroupP61619
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit beta96Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P60468
GTEx:  ENSG00000106803 
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UniProt GroupP60468
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gamma68Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P60059
GTEx:  ENSG00000132432 
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UniProt GroupP60059
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Signal peptide mix22Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alpha286Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000124783 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit beta183Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000163479 
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UniProt GroupP43308
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit gamma185Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  Q9UNL2
GTEx:  ENSG00000114850 
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UniProt GroupQ9UNL2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit delta173Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000180879 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A705Homo sapiensMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
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GTEx:  ENSG00000134910 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTC149Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000198856 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 437Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000228474 
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UniProt GroupP0C6T2
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 25879Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000134825 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1113Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000129562 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit456Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000244038 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1607Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000163902 
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UniProt GroupP04843
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2631Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P04844 (Homo sapiens)
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GTEx:  ENSG00000118705 
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UniProt GroupP04844
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTISOLDE
MODEL REFINEMENTCoot

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