8WHN | pdb_00008whn

Crystal Structure of the cytoplasmic domain of OST1 (Ribophorin I) from Candidatus Prometheoarchaeum syntrophicum strain MK-D1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.243 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries.

Carilo, I.Senju, Y.Yokoyama, T.Robinson, R.C.

(2024) J Biological Chem 300: 107673-107673

  • DOI: https://doi.org/10.1016/j.jbc.2024.107673
  • Primary Citation of Related Structures:  
    8WHN

  • PubMed Abstract: 

    In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.


  • Organizational Affiliation
    • Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribophorin 1 superfamily protein161Promethearchaeum syntrophicumMutation(s): 1 
Gene Names: DSAG12_02015
UniProt
Find proteins for A0A5B9DB24 (Promethearchaeum syntrophicum)
Explore A0A5B9DB24 
Go to UniProtKB:  A0A5B9DB24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5B9DB24
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.243 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.368α = 90
b = 58.708β = 90
c = 67.578γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20H00476
Simons FoundationUnited StatesGBMF9743
Other privateGBMF9743
Japan Science and TechnologyJapanJPMJCR19S5

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references