March 2006 Molecule of the Month by David Goodsell
Keywords: activation of blood coagulation via clotting cascade, clotting cascade, hemostatis, blood coagulation, factor VII, factor X
Blood performs many essential jobs in your body: it transports oxygen and nutrients, it protects your cells from infection, and it carries hormones and other messages from place to place in your body. But since blood is a liquid that is pumped under pressure, we must protect ourselves from leaks. Fortunately, the blood has a built-in repair method that quickly stops up breaks in the blood circulatory system as soon as they happen. You see these repairs in action whenever you cut yourself: the blood thickens and forms a gooey clot, which then dries into a scab that seals and protects the cut until it can heal.
To Clot or Not?
Blood clotting is a tricky business. All of the building blocks for a clot must be present all the time, so that they can instantly jump into action when damage occurs. But this must be done carefully and only at exactly the right time. If clots form in the wrong places, they could block the normal flow of blood, which could then cause heart attacks or strokes. Tissue factor is one of the molecules that triggers the formation of a clot when the time is right.
Inside Meets Outside
Your body uses a very simple method to sense when damage occurs. The cells in the neighborhood around blood vessels have tissue factor on their surfaces, but the cells that line the blood vessels do not. Most of the time, the blood flows smoothly through the vessels and never comes in contact with tissue factor. However, when you cut yourself, blood flows out of the vessels and into places that it shouldn't be. Then, it comes into contact with tissue factor, which starts the cascade that clots the escaping blood.
Looking at Tissue Factor
Tissue factor is a sausage-shaped protein that is tethered to the surface of cells. PDB entries 2hft (shown here) and 1boy show just the part on the outside of the cell. In the full-size protein, there is also a segment that crosses through the cell membrane and a small portion inside the cell. The portion outside is the part that interacts with the blood clotting machinery. The little bit inside, however, plays its own role in cell signaling. It is thought to be important for the control of cell migration as the wound is healing and new blood vessels are being built.
Tissue factor starts a cascade of interactions that lead to formation of a clot. The first step occurs when factor VII, which is found in the blood, binds to tissue factor. When it binds to tissue factor, as shown in PDB structure 1dan, it becomes almost a thousand times more active. It can then make a specific cut in factor X (shown here from PDB entries 1xka and 1iod), changing it into an active form. Factor X then activates thrombin, which then creates the fibrin that forms the fibrous structure of the clot. The trick to this cascading process is that a few molecules of tissue factor and factor VII can activate many copies of factor X, which can activate even more thrombin, which finally activates lots and lots of fibrin.
Exploring the Structure
As seen in PDB entry 1dan, factor VII embraces tissue factor, contacting the entire
length of the molecule. Factor VII has four domains strung together with flexible linkers.
At the bottom is the GLA domain, which has nine modified glutamic acids, labeled CGU
in the PDB structure file. These modified amino acids have an extra carboxylic acid
group that traps calcium ions. The ions interact with the membrane surface,
helping factor VII find tissue factor. The uppermost domain of factor VII is a protein-
cutting enzyme that will make the break in the factor X. This domain looks very much
like other serine proteases such as
In the middle are two small
domains that assist with the recognition of tissue factor. The small molecule in green is
an inhibitor that blocks the active site and thus acts as an anticoagulant that stops blood
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Additional information on tissue factor and blood clotting
H. R. Roberts, D. M. Monroe, M. Hoffman (2006) Molecular biology and biochemistry of the coagulation factors and pathways of hemostasis. Chapter 106 in: Williams Hematology, Seventh Edition. McGraw-Hill.
© 2014 David Goodsell & RCSB Protein Data Bank