PDBsum entry 1deq

Blood clotting

PDB id: 1deq

Contents

Protein chains

180 a.a.*

380 a.a.*

370 a.a.*

90 a.a.*

* C-alpha coords only

References listed in PDB file

Key reference

Title

The crystal structure of modified bovine fibrinogen.

Authors

J.H.Brown, N.Volkmann, G.Jun, A.H.Henschen-Edman, C.Cohen.

Ref.

Proc Natl Acad Sci U S A, 2000, 97, 85-90. [DOI no: 10.1073/pnas.97.1.85]

PubMed id

10618375

Abstract

Here we report the crystal structure at approximately 4-A resolution of a selectively proteolyzed bovine fibrinogen. This key component in hemostasis is an elongated 340-kDa glycoprotein in the plasma that upon activation by thrombin self-assembles to form the fibrin clot. The crystals are unusual because they are made up of end-to-end bonded molecules that form flexible filaments. We have visualized the entire coiled-coil region of the molecule, which has a planar sigmoidal shape. The primary polymerization receptor pockets at the ends of the molecule face the same way throughout the end-to-end bonded filaments, and based on this conformation, we have developed an improved model of the two-stranded protofibril that is the basic building block in fibrin. Near the middle of the coiled-coil region, the plasmin-sensitive segment is a hinge about which the molecule adopts different conformations. This segment also includes the boundary between the three- and four-stranded portions of the coiled coil, indicating the location on the backbone that anchors the extended flexible Aalpha arm. We suggest that a flexible branch point in the molecule may help accommodate variability in the structure of the fibrin clot.

Figure 2.
Fig. 2. Conformational flexibility of fibrinogen in the crystals. The diagrams show superpositions of noncrystallographically related fibrinogen molecules based on the least-squares fit of the relatively rigid coiled-coil segment: A 104-A 154, B 140-B 190, 77- 127. Among the different noncrystallographically related copies, the rms difference between the coordinates of this segment is about half that of the backbone's most flexible segment: A 64-A 114, B 100-B 150, 37- 87. (a) View, as in Fig. 1a, of one pair of molecules whose conformations differ primarily by bending within the plane of the sigmoidal coiled-coil axis. (b) View, as in Fig. 1b, of a different pair of molecules whose conformations differ primarily by bending out of the plane of the sigmoidal axis.

Figure 3.
Fig. 3. Conserved end-to-end molecular interactions. (a) Superposition of six -domain dimers derived from the various crystals of modified bovine fibrinogen (red) and human fragment D and crosslinked D-dimer (blue) (24, 25) show the domains to be similarly "offset" from one another. This feature can be visualized by noting, for example, that 264 of the right monomer is interacting at the edge of the - interface whereas in the left monomer it is interacting at the center of the interface. No significant difference in the offset is found among the three bovine -domain dimers or among the three human -domain dimers (pooled intra-species SD is 0.455 Å). Interspecies amino acid differences at or near the interface (e.g., 264, which is methionine in human and serine in bovine fibrinogen) probably perturb the docking of the domains, creating a slightly less staggered offset ( 1.7-Å rms difference) in the bovine -dimer relative to that in the human dimer. (b) Crystal structure of an end-to-end bonded fibrinogen filament. All -domain receptor pockets (shown by arrows) are on the same face of the extended filament.

Secondary reference #1

Title

Fibrinogen structure in projection at 18 a resolution. Electron density by co-Ordinated cryo-Electron microscopy and X-Ray crystallography.

Authors

S.P.Rao, M.D.Poojary, B.W.Elliott, L.A.Melanson, B.Oriel, C.Cohen.

Ref.

J Mol Biol, 1991, 222, 89-98.

PubMed id

1942070

Secondary reference #2

Title

Crystals of modified fibrinogen: size, Shape and packing of molecules.

Authors

J.W.Weisel, S.G.Warren, C.Cohen.

Ref.

J Mol Biol, 1978, 126, 159-183. [DOI no: 10.1016/0022-2836(78)90357-1]

PubMed id

739546

Figure 4.
IG. 4. Sodium dodecyl sulfate/acrylmide gel electrophoresis patt,erns of native and modified. fibrinoens. Protein samples were made up to 1% (a-/v) dodecyl sulfate, 1% (v/v) /3-ercap- toethanol, 0.01 x-phosphate (pH 7) and boiled for 5 min before electrophoresis. %or diestion conditions and other data see Table 2.

Figure 9.
FIG. 9. Diagram of shrinkage states of the P2, crystal lattice from X-ray diffraction measure- ments, showing that the [ -3,0,1] diagonal length is preserved in t,he various lattices. (See also Pig. 3 and Tble 1.)

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Crystalline states of a modified fibrinogen.

Authors

N.M.Tooney, C.Cohen.

Ref.

J Mol Biol, 1977, 110, 363-385. [DOI no: 10.1016/S0022-2836(77)80077-6]

PubMed id

845954

Figure 4.
FIG. 4. Microcrystals f modifiedfibrinogen precipitated a low ionic strength. (a), (b) and (d) Obliquely striated mierocrystals. Theaxial periods are 450 A. (e) Diagonal mierocrystal. The spaeings of the striations are about 85 A. Magnification = 165,000 .

Figure 6.
Fro. 6. Fibrin-like forms. ThisFigure illustrates the similarity of fibrous aggregates of naive and modified fibrinogcn, clotted with thrombin o precipitated at high ionic strength. Modified ibrinogen was digested in the range shwn in Table 1. Theaxialperlod of all forms is 225 A. (a) Fibrinogen precipitated at high ionio strength (0.3 M-KF, 0.01 M-N-tri(hydroxymethyl) methyl-2-amino ethane sulfonic acid, pH 7.5). Identical fibers were obtained by precipitation with Ba 2+, as decribed in (d and (e). (b) Fibrin prepared by clotting native fibrinogen with thrombin in 0.3 M-NaC1, 0.03 M-phosphate (pH 7.) directly on the grid. (e) Fibrin prepared by clottng modified fibrinogen in 0'3 M-NaC1, 0'03 M-phosphate (pH 7.5 directly on the grid. The central thin light band in the repeat of this and the following two speci- mens is less prominent than the corresponding band in fibes of native fibrinogen or fibrin.

The above figures are reproduced from the cited reference with permission from Elsevier