Rpn11 homolog from Caldiarchaeum Subterraneum

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.

Fuchs, A.C.D.Maldoner, L.Wojtynek, M.Hartmann, M.D.Martin, J.

(2018) Nat Commun 9: 2696-2696

  • DOI: https://doi.org/10.1038/s41467-018-05198-1
  • Primary Citation of Related Structures:  
    6FJ7, 6FJU, 6FJV, 6FNN, 6FNO

  • PubMed Abstract: 

    While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.

  • Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit N11-like protein
A, B
228Candidatus Caldarchaeum subterraneumMutation(s): 0 
Gene Names: CSUB_C1473HGMM_F04B03C04HGMM_F21D07C20HGMM_F30C12C32
Find proteins for E6N8B9 (Caldiarchaeum subterraneum)
Explore E6N8B9 
Go to UniProtKB:  E6N8B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6N8B9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.452α = 90
b = 65.614β = 90
c = 99.708γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description