SH3 Domain
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Description

SH3 domain #1NEB. Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.

Publication Date

1-23-2013

Keywords

biochemistry, protein, teaching

Disciplines

Biochemistry | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Life Sciences | Molecular Biology

Instructions

Students learn in many different ways. One important way to learn is tactile. Some people learn best by actually touching three-dimensional models. In biochemistry classes, students usually visualize protein structures using programs such as pymol, rasmol etc. For teaching protein structure and function, I have paired 3D printed models with pymol visualization in an iPad.

There are over 40 different protein domains. The three dimensional structure of proteins and their domains is determined by x-ray crystallography or nuclear magnetic resonance (NMR). The 3D coordinates of each atom in a domain is determined and provided in a protein database (PDB) format. The PDB files for every protein structure ever determined are freely available at PDB.org. Below is an explanation of how to take a PDB file and convert it to an STL file.

Convert pdb to stl file

Select structure from pdb.org

open VMD 1.9.1 (ks.uiuc.edu/Research/vmd/)

Load pdb file →file “new molecule”

“graphics” → representations → drawing method “tube”

Radius 1.5

Resolution 10

Display →axes → off

File→ render → “enter file name” → STL → render

Open in replicator G

Scale to appropriate size (many times very small and unseeable!)

Upload to cloud.nettfabb.com to fix stl

Slice and print!

Creative Commons License

Creative Commons Attribution 3.0 License
This work is licensed under a Creative Commons Attribution 3.0 License.

SH3 Domain

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