3WWV

C-terminal domain of stomatin operon partner protein 1510-C from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly

Yokoyama, H.Matsui, I.

(2014) FEBS Open Bio 4: 804-812

  • DOI: 10.1016/j.fob.2014.09.002
  • Primary Citation of Related Structures:  
    3WWV

  • PubMed Abstract: 
  • Stomatin, prohibitin, flotillin, and HflK/C (SPFH) domain proteins are found in the lipid raft microdomains of various cellular membranes. Stomatin/STOPP (stomatin operon partner protein) gene pairs are present in both archaeal and bacterial species, and their protein products may be involved in the quality control of membrane proteins ...

    Stomatin, prohibitin, flotillin, and HflK/C (SPFH) domain proteins are found in the lipid raft microdomains of various cellular membranes. Stomatin/STOPP (stomatin operon partner protein) gene pairs are present in both archaeal and bacterial species, and their protein products may be involved in the quality control of membrane proteins. In the present study, the crystal structure of the C-terminal soluble domain of STOPP PH1510 (1510-C) from the hyperthermophilic archaeon Pyrococcus horikoshii was determined at 2.4 Å resolution. The structure of 1510-C had a compact five-stranded β-barrel fold known as an oligosaccharide/oligonucleotide-binding fold (OB-fold). According to crystal packing, 1510-C could assemble into multimers based on a dimer as a basic unit. 1510-C also formed a large cylinder-like structure composed of 24 subunits or a large triangular prism-like structure composed of 12 subunits. These results indicate that 1510-C functions as a scaffold protein to form the multimeric assembly of STOPP and stomatin.


    Related Citations: 
    • Clustering of OB-fold domains of the partner protease complexed with trimeric stomatin from Thermococcales
      Yokoyama, H., Matsui, E., Hiramoto, K., Forterre, P., Matsui, I.
      (2013) Biochimie 95: 1494

    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Stomatin operon partner proteinA80Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH1510
EC: 3.4.21
UniProt
Find proteins for O59179 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59179 
Go to UniProtKB:  O59179
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.847α = 90
b = 75.847β = 90
c = 43.631γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2015-01-21
    Changes: Database references