2CF4

Pyrococcus horikoshii TET1 peptidase can assemble into a tetrahedron or a large octahedral shell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Archaeal Peptidase Assembles Into Two Different Quaternary Structures: A Tetrahedron and a Giant Octahedron.

Schoehn, G.Vellieux, F.M.D.Dura, M.A.Receveur-Brechot, V.Fabry, C.M.S.Ruigrok, R.W.H.Ebel, C.Roussel, A.Franzetti, B.

(2006) J Biol Chem 281: 36327

  • DOI: https://doi.org/10.1074/jbc.M604417200
  • Primary Citation of Related Structures:  
    2CF4

  • PubMed Abstract: 

    Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.


  • Organizational Affiliation

    Laboratoire de Virologie Moléculaire et Structurale c/o EMBL, FRE 2854 CNRS-UJF, 38042 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PH0519332Pyrococcus horikoshii OT3Mutation(s): 0 
EC: 3.4.11
UniProt
Find proteins for O58255 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58255 
Go to UniProtKB:  O58255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58255
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.88α = 90
b = 221.88β = 90
c = 221.88γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SELDATdata scaling
SCALKB2data scaling
KBAPLYdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description