PDBsum entry 1deq

Blood clotting

PDB id: 1deq

Contents

Protein chains

180 a.a.* *

380 a.a.* *

370 a.a.* *

90 a.a.* *

* Residue conservation analysis

* C-alpha coords only

PDB id:

1deq

Name:

Blood clotting

Title:

The crystal structure of modified bovine fibrinogen (at ~4 angstrom resolution)

Structure:

Fibrinogen (alpha chain). Chain: a, d, n, q. Fragment: pseudomonas aeruginosa ps-1-modified fragment. Fibrinogen (beta chain). Chain: b, e, o, r. Fragment: pseudomonas aeruginosa ps-1-modified fragment. Fibrinogen (gamma chain). Chain: c, f, p, s. Fragment: pseudomonas aeruginosa ps-1-modified fragment.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913

Biol. unit:

Heptamer (from PQS)

Resolution:

3.50Å R-factor: 0.257 R-free: 0.370

Authors:

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

Key ref:

J.H.Brown et al. (2000). The crystal structure of modified bovine fibrinogen. Proc Natl Acad Sci U S A, 97, 85-90. PubMed id: 10618375 DOI: 10.1073/pnas.97.1.85

Date:

15-Nov-99 Release date: 02-Feb-00

Protein chains

P02672  (FIBA_BOVIN) -  Fibrinogen alpha chain from Bos taurus

Seq: 615 a.a.

Struc: 180 a.a.*

Protein chains

P02676  (FIBB_BOVIN) -  Fibrinogen beta chain from Bos taurus

Seq: 468 a.a.

Struc: 380 a.a.*

Protein chains

P12799  (FIBG_BOVIN) -  Fibrinogen gamma-B chain from Bos taurus

Seq: 444 a.a.

Struc: 370 a.a.*

Protein chains

No UniProt id for this chain

Struc: 90 a.a.

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

reference

DOI no: 10.1073/pnas.97.1.85

Proc Natl Acad Sci U S A 97:85-90 (2000)

PubMed id: 10618375

The crystal structure of modified bovine fibrinogen.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.