8BF9 | pdb_00008bf9

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

Karki, S.Javanainen, M.Rehan, S.Tranter, D.Kellosalo, J.Huiskonen, J.T.Happonen, L.Paavilainen, V.

(2023) EMBO Rep 24: e57910-e57910

  • DOI: https://doi.org/10.15252/embr.202357910
  • Primary Citation Related Structures: 
    8BF9

  • PubMed Abstract: 

    Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.


  • Organizational Affiliation
    • Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Macromolecule Content 

  • Total Structure Weight: 1,548.69 kDa 
  • Atom Count: 55,482 
  • Modeled Residue Count: 3,914 
  • Deposited Residue Count: 6,564 
  • Unique protein chains: 17
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alphaC [auth A]353Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6NUI6 (Ovis aries)
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UniProt GroupA0ACI6NUI6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit betaD [auth B]186Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit deltaE [auth D]173Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6S0U3 (Ovis aries)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit gammaF [auth G]185Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6QJ47 (Ovis aries)
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UniProt GroupA0ACI6QJ47
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22G [auth P]184Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6NK20 (Ovis aries)
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UniProt GroupA0ACI6NK20
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L19H [auth R]196Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6PJ70 (Ovis aries)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
RL22 protein (Fragment)I [auth U]128Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6P7EJM7 (Ovis aries)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L23/L25 N-terminal domain-containing proteinJ [auth X]156Ovis ariesMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
RL26 protein (Fragment)K [auth Y]134Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6P3ED73 (Ovis aries)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Sec61aL [auth C]475Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Sec61bM [auth b]29Ovis ariesMutation(s): 0 
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31N [auth d]125Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6PCP1 (Ovis aries)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaO [auth g]81Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A836CVU8 (Ovis aries)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29P [auth h]123Ovis ariesMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L37Q [auth j]97Ovis ariesMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38R [auth k]70Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0ACI6QYF0 (Ovis aries)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39S [auth l]51Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6P3TG10 (Ovis aries)
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UniProt GroupA0A6P3TG10
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (1766)A [auth 5]3,662Ovis aries
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (156-MER)B [auth 8]156Ovis aries
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
M [auth b]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland338836
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-07-02
    Changes: Data collection