3BK6

Crystal structure of a core domain of stomatin from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold

Yokoyama, H.Fujii, S.Matsui, I.

(2008) J.Mol.Biol. 376: 868-878

  • DOI: 10.1016/j.jmb.2007.12.024

  • PubMed Abstract: 
  • Stomatin is a major integral membrane protein of human erythrocytes, the absence of which is associated with a form of hemolytic anemia known as hereditary stomatocytosis. However, the function of stomatin is not fully understood. An open reading fra ...

    Stomatin is a major integral membrane protein of human erythrocytes, the absence of which is associated with a form of hemolytic anemia known as hereditary stomatocytosis. However, the function of stomatin is not fully understood. An open reading frame, PH1511, from the hyperthermophilic archaeon Pyrococcus horikoshii encodes p-stomatin, a prokaryotic stomatin. Here, we report the first crystal structure of a stomatin ortholog, the core domain of the p-stomatin PH1511p (residues 56-234 of PH1511p, designated as PhSto(CD)). PhSto(CD) forms a novel homotrimeric structure. Three alpha/beta domains form a triangle of about 50 A on each side, and three alpha-helical segments of about 60 A in length extend from the apexes of the triangle. The alpha/beta domain of PhSto(CD) is partly similar in structure to the band-7 domain of mouse flotillin-2. While the alpha/beta domain is relatively rigid, the alpha-helical segment shows conformational flexibility, adapting to the neighboring environment. One alpha-helical segment forms an anti-parallel coiled coil with another alpha-helical segment from a symmetry-related molecule. The alpha-helical segment shows a heptad repeat pattern, and mainly hydrophobic residues form a coiled-coil interface. According to chemical cross-linking experiments, PhSto(CD) would be able to assemble into an oligomeric form. The coiled-coil fold observed in the crystal probably contributes to self-association.


    Related Citations: 
    • Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii
      Yokoyama, H.,Matsui, E.,Akiba, T.,Harata, K.,Matsui, I.
      (2006) J.Mol.Biol. 358: 1152


    Organizational Affiliation

    School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PH stomatin
A, B, C
188Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)N/A
Find proteins for O59180 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59180
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.553α = 90.00
b = 137.150β = 107.61
c = 58.544γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance