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About the
RCSB PDB Molecule of the Month
Using selected molecules from the PDB
archive, each feature includes an introduction
to the structure and function of the molecule,
a discussion of its relevance to human health
and welfare, and suggestions for viewing and
accessing further details.
The RCSB PDB Molecule of the Month is
read by students, teachers, and scientists
worldwide at www.pdb.org.
This April 2000 edition was written and
illustrated by David S. Goodsell
(RCSB PDB and The Scripps
Research Institute).
MOLECULE OF THE MONTH:
COLLAGEN
The Collagen Triple Helix
Collagen is composed of three chains, wound
together in a tight triple helix. The illustration
included here shows only a small segment of the
entire moleculeeach chain is over 1400 amino
acids long and only about 20 are shown here. A
repeated sequence of three amino acids forms
this sturdy structure. Every third amino acid is
glycine, a small amino acid that fits perfectly
inside the helix. Many of the remaining posi-
tions in the chain are filled by two unexpected
amino acids: proline and a modified version of
proline, hydroxyproline. We wouldn't expect
proline to be this common, because it forms a
kink in the polypeptide chain that is difficult to
accommodate in typical globular proteins. But,
as you can see on the next page, it seems to be
just the right shape for this structural protein.
Vitamin C
Hydroxyproline, which is critical for collagen
stability, is created by modifying normal proline
amino acids after the collagen chain is built. The
reaction requires vitamin C to assist in the addi-
tion of oxygen. Unfortunately, we cannot make
vitamin C within our bodies, and if we don't get
enough in our diet, the results can be disastrous.
Vitamin C deficiency slows the production of
hydroxyproline and stops the construction of
new collagen, ultimately causing scurvy. The
symptoms of scurvyloss of teeth and easy bruis-
ingare caused by the lack of collagen to repair the
wear-and-tear caused by everyday activities.
Collagen on the Grocery Shelf
Collagen from livestock animals is a familiar
ingredient for cooking. Like most proteins,
when collagen is heated, it loses all of its struc-
ture. The triple helix unwinds and the chains
separate. Then, when this denatured mass of tan-
gled chains cools down, it soaks up all of the sur-
rounding water like a sponge, forming gelatin.
Ropes and Ladders
We make many different kinds of collagen,
which form long ropes and tough sheets that are
used for structural support in mature animals
and as pathways for cellular movement during
development. All contain a long stretch of triple
helix connected to different types of ends. The
simplest is merely a long triple helix, with blunt
Your Most Plentiful Protein
About one quarter of all of the protein in your body is
collagen. Collagen is a major structural protein, forming
molecular cables that strengthen the tendons and vast,
resilient sheets that support the skin and internal organs.
Bones and teeth are made by adding mineral crystals to
collagen. Collagen provides structure to our bodies,
protecting and supporting the softer tissues and connecting
them with the skeleton. But, in spite of its critical function
in the body, collagen is a relatively simple protein.
RCSB Protein Data Bank
The Protein Data Bank (PDB) is the
single worldwide repository for the
processing and distribution of 3D
structure data of large molecules of
proteins and nucleic acids. The RCSB
PDB is operated by Rutgers, The State
University of New Jersey and the San
Diego Supercomputer Center and the
Skaggs School of Pharmacy and
Pharmaceutical Sciences at the University
of California, San Diegotwo members
of the Research Collaboratory for
Structural Bioinformatics (RCSB).
It is supported by funds from the
National Science Foundation, the
National Institute of General Medical
Sciences, the Office of Science,
Department of Energy, the National
Library of Medicine, the National
Cancer Institute, the National Institute
of Neurological Disorders and Stroke
and the National Institute of Diabetes
& Digestive & Kidney Diseases.
The RCSB PDB is a member of
the worldwide PDB
(wwPDB; www.wwpdb.org).
References:
1cag: J. Bella, M. Eaton, B. Brodsky, H. M. Berman
(1994) Crystal and molecular structure of a collagen-
like peptide at 1.9 A resolution. Science 266: 75-81
1bkv: R. Z. Kramer, J. Bella, P. Mayville, B. Brodsky,
H. M. Berman (1999) Sequence dependent conforma-
tional variations of collagen triple-helical structure.
Nat.Struct.Biol. 6: 454-457
COLLAGEN
A special amino acid sequence makes the tight colla-
gen triple helix particularly stable. Every third amino
acid is a glycine, and many of the remaining amino
acids are proline or hydroxyproline. A classic triple
helix is shown here, and may be viewed in the PDB
file 1cag. Notice how the glycine forms a tiny elbow
packed inside the helix, and notice how the proline
and hydroxyproline smoothly bend the chain back
around the helix. In this structure, the researchers
placed a larger alanine amino acid in the position nor-
mally occupied by glycine, showing that it crowds the
neighboring chains.
This collagen helix contains a segment of human
collagen, and may be viewed in the PDB file 1bkv.
Notice that the top half is very uniform, where the
sequence is the ideal mixture of glycine and pro-
lines. At the bottom, the helix is less regular,
because many different amino acids are placed
between the equally-spaced glycines.
ends. These "type I" collagen molecules associate
side-by-side, like fibers in a rope, to form tough fib-
rils. These fibrils crisscross the space between nearly
every one of our cells.
The illustration above depicts a basement mem-
brane, which forms a tough surface that supports
the skin and many organs. A different collagen
"type IV"forms the structural basis of this mem-
brane. Type IV collagen has a globular head at one
end and an extra tail at the other. The heads bind
strongly together, head-to-head, and four collagen
molecules associate together through their tails,
forming an X-shaped complex. Using these two
types of interactions, type IV collagen forms an
extended network, shown here in light blue. Two
other moleculescross-shaped laminin (blue-
green) and long, snaky proteoglycans (green)fill
in the spaces, forming a dense sheet.
Exploring the Structure
1cag
1bkv