PDBsum entry: 3bk6

Membrane protein

PDB id: 3bk6

Contents

Protein chains

170 a.a. *

142 a.a. *

160 a.a. *

* Residue conservation analysis

PDB id:

3bk6

Name:

Membrane protein

Title:

Crystal structure of a core domain of stomatin from pyrococcus horikoshii

Structure:

Ph stomatin. Chain: a, b, c. Fragment: residues 56-234. Synonym: p-stomatin ph1511. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph1511. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.20Å R-factor: 0.204 R-free: 0.262

Authors:

H.Yokoyama,S.Fujii,I.Matsui

Key ref:

H.Yokoyama et al. (2008). Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold. J Mol Biol, 376, 868-878. PubMed id: 18182167 DOI: 10.1016/j.jmb.2007.12.024

Date:

05-Dec-07 Release date: 19-Feb-08

Protein chain

O59180  (Y1511_PYRHO) -  Uncharacterized protein PH1511

Seq: 266 a.a.

Struc: 170 a.a.*

Protein chain

O59180  (Y1511_PYRHO) -  Uncharacterized protein PH1511

Seq: 266 a.a.

Struc: 142 a.a.*

Protein chain

O59180  (Y1511_PYRHO) -  Uncharacterized protein PH1511

Seq: 266 a.a.

Struc: 160 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)

DOI no: 10.1016/j.jmb.2007.12.024

J Mol Biol 376:868-878 (2008)

PubMed id: 18182167

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

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

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 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.

Selected figure(s)

Figure 1.
Fig. 1. Stereo representation of the 2F[o] − F[c] electron densities of PhSto^CD contoured at 1.5σ. The inner side of the α/β domain of chain A is shown. Each residue is shown as a stick model (C atom, yellow; N atom, blue; O atom, red).

Figure 3.
Fig. 3. Superposition of the Cα traces of PhSto^CD and the mouse flotillin-2 band-7 domain (stereoview). The monomer (chain A) of PhSto^CD is shown in cyan, and the flotillin-2 band-7 domain (PDB code 1win) is shown in orange.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 376, 868-878) copyright 2008.

Figures were selected by an automated process.