6FNN

Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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

  • 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 ...

    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. joerg.martin@tuebingen.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit N11-like proteinA, B155Candidatus Caldarchaeum subterraneumMutation(s): 0 
Gene Names: CSUB_C1473HGMM_F04B03C04HGMM_F21D07C20HGMM_F30C12C32
EC: 3.4.19.12
UniProt
Find proteins for E6N8B9 (Caldiarchaeum subterraneum)
Explore E6N8B9 
Go to UniProtKB:  E6N8B9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like proteinC, D104Candidatus Caldarchaeum subterraneumMutation(s): 0 
Gene Names: CSUB_C1474HGMM_F04B03C03HGMM_F21D07C21HGMM_F30C12C33
UniProt
Find proteins for E6N8B8 (Caldiarchaeum subterraneum)
Explore E6N8B8 
Go to UniProtKB:  E6N8B8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], H [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.674α = 90
b = 94.571β = 90
c = 170.855γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release