PDBsum entry 1txh

Membrane protein

PDB id: 1txh

Contents

Protein chains

(+ 0 more) 86 a.a.*

* C-alpha coords only

Theoretical model

PDB id:

1txh

Name:

Membrane protein

Title:

A theoretical c-alpha model of the transmembrane alpha- helices in gap junction intercellular channels

Structure:

Gap junction beta-1 protein. Chain: a, b, c, d, e, f. Fragment: transmembrane domain. Synonym: connexin 32, cx32, gap junction 28 kda liver protein

Source:

Homo sapiens. Human

Authors:

S.J.Fleishman,V.M.Unger,M.Yeager,N.Ben-Tal

Key ref:

S.J.Fleishman et al. (2004). A Calpha model for the transmembrane alpha helices of gap junction intercellular channels. Mol Cell, 15, 879-888. PubMed id: 15383278 DOI: 10.1016/j.molcel.2004.08.016

Date:

05-Jul-04 Release date: 28-Sep-04

Protein chains

P08034  (CXB1_HUMAN) -  Gap junction beta-1 protein from Homo sapiens

Seq: 283 a.a.

Struc: 86 a.a.

Key reference

DOI no: 10.1016/j.molcel.2004.08.016

Mol Cell 15:879-888 (2004)

PubMed id: 15383278

A Calpha model for the transmembrane alpha helices of gap junction intercellular channels.

S.J.Fleishman, V.M.Unger, M.Yeager, N.Ben-Tal.

ABSTRACT

Gap junction channels connect the cytoplasms of apposed cells via an intercellular conduit formed by the end-to-end docking of two hexameric hemichannels called connexons. We used electron cryomicroscopy to derive a three-dimensional density map at 5.7 angstroms in-plane and 19.8 angstroms vertical resolution, allowing us to identify the positions and tilt angles for the 24 alpha helices within each hemichannel. The four hydrophobic segments in connexin sequences were assigned to the alpha helices in the map based on biochemical and phylogenetic data. Analyses of evolutionary conservation and compensatory mutations in connexin evolution identified the packing interfaces between the helices. The final model, which specifies the coordinates of Calpha atoms in the transmembrane domain, provides a structural basis for understanding the different physiological effects of almost 30 mutations and polymorphisms in terms of structural deformations at the interfaces between helices, revealing an intimate connection between molecular structure and disease.

Selected figure(s)

Figure 1.
Figure 1. Overlay of Cross-Sections of the 3D Density Map of One Connexon Derived by Electron CryocrystallographyCounting from the middle of the extracellular gap and toward the observer, sections +14, +18, and +24 (A) and +20, +24, +29, and +34 (B) were used. The approximate boundary between the membrane and the extracellular gap corresponds to section +8 (not shown). The vertical distance between consecutive sections is 2 Å. Densities belonging to the same helices are represented by the same base color, with the darkest and lightest shades corresponding to densities in sections +14 and +34, respectively. Helices were arbitrarily marked A–D and A′ and B′ (which are symmetry related to A and B) to provide a reference for discussion. The position marked (0,0) was used to generate grid coordinates for the locations of helices A–D given in Table 1. The spacing between grid lines is 10 Å, and the map was contoured starting at 1.5σ above the mean.

Figure 5.
Figure 5. Structural Features of the TM Domain of the Gap Junction Connexon(A) Polar and charged amino acid residues in the protein interior. The polar residues (yellow spheres) are roughly in register and could be involved in the formation of a network of hydrogen bonds that would stabilize interhelical contacts.(B) Acidic and basic residues in the protein interior and facing the pore lumen are indicated by red and blue spheres, respectively. Arg22 is near the boundary of the hydrophobic domain and could be accessible to the cytoplasmic side of the membrane (von Heijne, 1989). Glu208 also resides at this boundary and is likely to be exposed to the cytoplasm. The pore-lining charged residues form a slender (4–5 Å) belt of charge around the pore lumen. None of the charged residues is exposed to the membrane.(C) Aromatic residues on M3 and M4 are shown as purple spheres. The two Phe positions on M4 coincide with the position of a protrusion of density on helix D in the cryo-EM map (Unger et al., 1999). Stacked aromatic residues have been shown to generate such protrusions of density (Henderson et al., 1990). The clustering of aromatic residues from M3 and M4 could stabilize interhelical contacts. Furthermore, the ridge of aromatic residues on M3 could serve to shield the water-filled pore from the lipids in this region of the protein structure, in which helices are not tightly packed.

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 15, 879-888) copyright 2004.