Summary of the Packing
in the Known Membrane Protein Structures

Membrane Protein Organism PDB Protein Atoms Buried Atoms Vol. Buried (cubic A) Ref. Vol. Buried Rel. Pack. Eff.
Bacteriorhodopsin H. halobium 2brd 1718 597 7889 8030 98.3%
Cytochrome bc1 complex B. taurus 1bgy 31224 9963 130467 132866 98.2%
Cytochrome c oxidase P. denitrificans 1ar1 7926 3885 55934 56973 98.2%
"" B. taurus 2occ 28614 11321 157103 157777 99.6%
Fumarate reductase E. coli 1fum 16598 6332 86085 87894 97.9%
Glycophorin A H. sapiens 1afo 628 101 1087 1221 89.0%
K+ channel S. lividans 1bl8 2824 1006 12881 13466 95.7%
Light-harvesting complex R. molischianum 1lgh 3096 1383 19120 19546 97.8%
Mechanosensitive ion channel M. tuberculosis 1msl 3945 830 9951 10497 94.8%
Photosynthetic reaction center R. spheroides 1aig 13014 5851 83595 84733 98.7%
"" R. viridis 1prc 9345 4488 63581 64592 98.4%

The packing at the buried interfaces in membrane proteins appears to be exceptionally tight. This table box shows a summary of the packing in 13 distinct membrane proteins structures that have been studied crystallographically. For each structure packing calculations were done on the buried protein atoms, where the buried atoms are subset of the total protein atoms, defined here as having less than 3 sq. A of surface area exposed to either lipid or water. The total Voronoi volume of these buried atoms was calculated by standard methods and then compared to the reference volumes that these atoms would occupy in the core of well-packed soluble protein structures (Tsai et al. J. Mol. Biol. 290: 253 (1999)). The relative packing efficiency is the ratio of these two numbers. It consistently indicates that buried membrane protein atoms occupy less space and are thus packed more efficiently than atoms in soluble protein cores. This is rather remarkable when on considers that the known membrane protein structures have been determined at relatively low-resolution, a fact often associated with looser packing in soluble proteins. Notes: 2brd was picked as representative instead of 1at9, 1ap9, and 1brd; 1bgy was picked instead of 1be3 and 1qcr; and 1aig, instead of 1aij and 1pcr. The parameter set used for all calculations, radii, typing scheme, and reference volumes, is the standard ProtOr set (Tsai et al. ibid.).

More Information

Expanded Summary Table

Data files giving packing in all membrane protein atoms

Data vs. ProtOr volumes

Data vs. BL- volumes

Last Updated on 8/17/99
Email: Mark.Gerstein@yale.edu