The structure of prothrombin fragment 1 at 3.5-A resolution.
The structure of prothrombin fragment 1 has been determined at 3.5-A resolution by multiple isomorphous replacement methods with four heavy atom derivatives. The final average figure of merit is 0.72. There is a large cylindrical solvent region with an average diameter of 35-40 A along the entire length of the c axis (85 A) centered at about x = y = 1/2. The connected density forming the wall of this channel is not of sufficient extent to account for the 156 residues of fragment 1 and the two accompanying carbohydrate chains totaling 5000 in molecular weight. Deglycosylated fragment 1 crystallizes isomorphously with fragment 1, and a difference map between the two revealed that the sugar chains are severely disordered and reside in the solvent channel. Although the disordered carbohydrate and the complexity of five disulfides in a 126-residue sequence have hampered the complete tracing of the peptide chain, two-thirds of the molecule has been accounted for in the form of an unusually oblate ellipsoid of about 15 X 30 X 35 A. The folding of the molecule has little secondary structure (one alpha-helix (7%), 20% beta-structure) in agreement with dichroism measurements and one of the points of carbohydrate attachment is suggested from the deglycosylated difference map.
D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D005583:Fourier Analysis; D008958:Models, Molecular; D008970:Molecular Weight; D010446:Peptide Fragments / Q000302:isolation & purification*; D011487:Protein Conformation; D011498:Protein Precursors; D011516:Prothrombin / Q000302:isolation & purification*; D014961:X-Ray Diffraction
D010446:Peptide Fragments; D011498:Protein Precursors; C029733:prothrombin fragment 1; D011516:Prothrombin