Department of Biochemistry,
University of Oxford,
South Parks Road,
t: 01865 613200
2020 Mark Howarth. All rights reserved.
Outreach: A protein alphabet
I was thinking about the diversity of protein shapes and so curated the alphabet below.
(Some of the lab’s research relates to building new protein architectures.)
Note that these are not structures from my lab- they come from groups around the world. It is those groups who did the hard
work! When academic researchers solve a protein structure, they make the structure freely available in the
Protein Data Bank
for anyone to look at and learn from. In the table below, I briefly describe the function of the protein and give a link to the PDB code,
so you can click on that code to easily find more about any structure that interests you. This alphabet was published in
Structural and Molecular Biology in May 2015
These structures are shown in cartoon format, which makes the overall path of the polypeptide chain easier to see; alpha-helices are
shown as coils and beta-strands are shown as arrows. The structures are coloured with the N-terminus of each chain in blue and the C-
terminus in red.
Movie of protein alphabet rotating
or watch on
Can you help?
- What other alphabets are there representing shapes in science? I know of one from Kjell Bloch Sandved finding the
Also, alphabets of human cell
, tissues from
- Do you know
protein structures matching well to letters or numbers? (O and C are relatively easy to find. B, E, F, G, H, K, and R
are hard to find.)
Videos for non-scientists
What is a Protein?
Learn about the 3D shape and function of macromolecules.
Introduction to crystallography
through cartoons from the Royal Institution.
From Protein to Crystal
by Prof. Elspeth Garman from our Department.
Protein alphabet resources
Please use these files freely for any non-commercial purposes. Copyright on files is mine, so you don’t need journal permission.
- Just type in to spell out words in Protein Alphabet- converter on
webpage from NIH
- Complete protein alphabet image (as above)
Low res jpg
- Editable protein alphabet image so easy to re-arrange letters in
, or as .xcf (
9MB) for more control using the
GNU Image Manipulation Program
- All individual protein letters (
of .pse files 15 MB) for viewing 3D structures with PyMOL software.
- Movie as
(14 MB) or
- Protein Letter
from Christian Hesketh
Table of the protein alphabet
Click on the PDB code to go to the primary research paper. Hyperlinks on the right are helpful background.
PDB code Function
DNA gyrase reaction core from
Target of antibiotic.
-like protein from
Blocks RNA degradation
Ribonuclease will bind in centre super-tight.
Pore to export
) in outer membrane of
Non-pore subunits cut from the image.
Milk sugar metabolism
Tagatose-6-phosphate kinase from
Myosin fragment bound to regulatory chains, from chicken.
of 2D array.
. Mimic of a protein in eukaryotic defence.
from human. 15
Keratin-like domain of
from the model plant,
Elongation Factor P
. Three β-barrels,
mimicking negative charge and L-shape of
Human enzyme adding CCA trinucleotide to 3’ end of
and 3-layer sandwich
cytolysin A from
. 12 copies of 3-helix bundle.
Development of nerves
6A extracellular domain from mouse.
and blood vessels
outer membrane channel.
A bound to a fragment of follistatin.
Human transportin recognizing a
nuclear localization signal.
GAF domain from
Blood vessel formation
Vascular Endothelial Growth Factor
bound to neutralizing antibody fragment.
Metal ion transport
through inner membrane into the cytoplasm.
DNA-binding domain from
Modular DNA-binding specificity useful for
domain of N-acetylglucosamine
from mouse. The arms can flex to recognize different targets.
Part of collagen
from human, relating to role of
Vitamin C in preventing