Figure 3.
Comparison of FVa and APC in the complex with other structures. (A) Cartoon rendering of the structure of FVa in the FVa-APC complex (cyan) overlaid with that of FVa in the prothrombinase complex (brown; left, PDB 9CTH)5,7 or free FVa (magenta; right, PDB 7KXY).4 Relevant PDB files used in the overlays are noted. Differences induced by APC binding (RMSD of 3.97 Å over 1197 Cα atoms vs FVa in the prothrombinase complex, left; RMSD of 2.64 Å over 985 Cα atoms vs free FVa, right) include a slight upward shift of the loops facing the membrane in the C domains. In the A1 domain, the site of APC cleavage at R306 becomes more exposed (72% vs 32%) to solvent and the segment 305TRNLKKITREQRRHM319 (blue vs red in the aligned structures, top, and insets, bottom) is pushed upward >4 Å because of interaction with APC. The critical A2 domain containing the site of APC cleavage at R506 features a drastic displacement of the 654VKCIPDDDEDSYEIFEP670 latch that functions as an exosite ligand binding to APC (Figure 2; supplemental Figure 1). Residue R506 (insets) moves 10 Å relative to the position in the prothrombinase complex (left) or 15 Å relative to the position in free FVa (right) to dock into the APC active site (Figure 6). (B) Cartoon rendering of the structure of APC in the FVa-APC complex (cyan) overlaid with that of APC bound to PPACK (brown) and lacking the Gla domain.28,29 The 2 structures overlap considerably in the PD (RMSD of 0.81 Å over 197 Cα atoms), with catalytic residues, oxyanion hole, and primary specificity pocket well organized for catalysis. The most notable difference involves a drastic rearrangement of the autolysis loop 304SSREKEAKRNRTF316 (c145-c153; RMSD of 4.39 Å over 13 Cα atoms) induced by binding of the latch of FVa (Figure 5). The rest of the APC structure aligns well with the PPACK-bound form in the EGF2 domain but diverges drastically at the level of the EGF1 domain. The Gla domain of APC is resolved, to our knowledge, for the first time in the FVa-APC complex and is not aligned with the main axis of the protein. The curved arrangement is similar to that recently reported for FXa, bound to FVa in the prothrombinase complex5,7 or free in solution,62 and to the closed form of prothrombin.5,7,63 The arrangement is also consistent with single molecule measurements of APC.46

Comparison of FVa and APC in the complex with other structures. (A) Cartoon rendering of the structure of FVa in the FVa-APC complex (cyan) overlaid with that of FVa in the prothrombinase complex (brown; left, PDB 9CTH)5,7 or free FVa (magenta; right, PDB 7KXY).4 Relevant PDB files used in the overlays are noted. Differences induced by APC binding (RMSD of 3.97 Å over 1197 Cα atoms vs FVa in the prothrombinase complex, left; RMSD of 2.64 Å over 985 Cα atoms vs free FVa, right) include a slight upward shift of the loops facing the membrane in the C domains. In the A1 domain, the site of APC cleavage at R306 becomes more exposed (72% vs 32%) to solvent and the segment 305TRNLKKITREQRRHM319 (blue vs red in the aligned structures, top, and insets, bottom) is pushed upward >4 Å because of interaction with APC. The critical A2 domain containing the site of APC cleavage at R506 features a drastic displacement of the 654VKCIPDDDEDSYEIFEP670 latch that functions as an exosite ligand binding to APC (Figure 2; supplemental Figure 1). Residue R506 (insets) moves 10 Å relative to the position in the prothrombinase complex (left) or 15 Å relative to the position in free FVa (right) to dock into the APC active site (Figure 6). (B) Cartoon rendering of the structure of APC in the FVa-APC complex (cyan) overlaid with that of APC bound to PPACK (brown) and lacking the Gla domain.28,29 The 2 structures overlap considerably in the PD (RMSD of 0.81 Å over 197 Cα atoms), with catalytic residues, oxyanion hole, and primary specificity pocket well organized for catalysis. The most notable difference involves a drastic rearrangement of the autolysis loop 304SSREKEAKRNRTF316 (c145-c153; RMSD of 4.39 Å over 13 Cα atoms) induced by binding of the latch of FVa (Figure 5). The rest of the APC structure aligns well with the PPACK-bound form in the EGF2 domain but diverges drastically at the level of the EGF1 domain. The Gla domain of APC is resolved, to our knowledge, for the first time in the FVa-APC complex and is not aligned with the main axis of the protein. The curved arrangement is similar to that recently reported for FXa, bound to FVa in the prothrombinase complex5,7 or free in solution,62 and to the closed form of prothrombin.5,7,63 The arrangement is also consistent with single molecule measurements of APC.46 

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