Blogging a crystal structure a day in 2014


Contributed by

Anton Le Brun

A protein structure that is a β-barrel of laughs

What does it look like?

Outer membrane protein F (OmpF) from Escherichia coli

Outer membrane protein F (OmpF) from Escherichia coli.

What is it?

A membrane is the biological structure that forms the barrier between a cell and its outside environment. Gram-negative bacteria (so called because they don't respond to the Gram stain) have a double membrane and include bacteria such as Escherichia coli (the microbiologist's lab rat), Yersinia pestis (bubonic plague), and Pseudomonas aeruginosa (lung infections in cystic fibrosis patients). The outer membrane of Gram-negative bacteria forms a barrier that protects the cell from toxins and other harmful agents; however, vital nutrients still need to cross the outer membrane to get to the cell. The membrane proteins that facilitate nutrient transport across the outer membrane are known as porins. Shown here is the porin called outer membrane protein F (OmpF) from E. coli.

OmpF is a general porin that will allow small (generally under 600 Da) water-soluble molecules to passively cross the outer membrane. Typically an E. coli will have about 100 000 OmpF molecules per cell. OmpF is a homotrimer with each monomer consisting of 16 β-strands that form a hollow cylindrical structure called a β-barrel (hence today's title). Molecules travel down the centre of each β-barrel where there is also a constriction loop (parts coloured orange) which reduces the size of the pore to 1.7 nm in diameter.

Where does it come from?

The crystal structure of OmpF was first determined by S. Cowen and colleagues in 1992 [1] and the structure shown is OmpF in the tetragonal crystal form [2] and has the PBD number 1OPF in the protein data bank.

[1] S.W. Cowen, T. Schirmer, G. Rummel, M. Steiert, R. Ghosh, R.A. Pauptit, J.N. Jansonius, J.P. Rosenbush (1992) Crystal structures explain functional properties of two E. coli porins. Nature 358: 727-733.

[2] S.W. Cowen, R.M. Garavito, J.N. Jansonius, J.A. Jenkins, R. Karlsson, N. Konig, E.F. Pai, R.A. Pauptit, P.J. Rizkallah, J.P. Rosenbush, G. Rummel, T. Schirmer (1995) The structure of OmpF porin in a tetragonal crystal form. Structure 3: 1041-1050.

Tags: protein   membranes   biological