Protein Structure for PDB 3U8V

by MoleculeMaker, published

Protein Structure for PDB 3U8V by MoleculeMaker Mar 7, 2013
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4801Views 497Downloads Found in Biology


This is my second attempt to print out a protein structure based on a pdb file. This printed well, and is now a completed model. I am planning to paint it soon, and will post more later.
This protein is a simple protein with a series of 7 amino acid repeat motifs, highlighted by a histidine residue. The crystal structure revealed that these histidines form a 4 alpha helical bundle, and the histidines seem to form a zipper pattern. I built the model with these histidine residues displayed. This is a natural protein, found in the organism Nitrosomonas europaea, which is commonly found in wastewater treatment plants.


This structure is an extensive print. THIS CAN ONLY BE PRINTED WITH BOTH RAFT AND SUPPORT selected, and a word of warning, expect 5-6 hours to remove the support and get down to the actual model. I removed the supports as well, and am preparing to paint.. I am printing at medium quality. The build time was nearly 15 hours, so be warned, it takes some time. Also had some issues with the raft separating from the build plate, but with the supports included, this didn't seem to matter. I printed this out on a Makerbot Replicator 2.
The model took a good deal of effort to construct. The original pdb file (3U8V) was manipulated until only a single dimer with no water molecules was included. This was then placed into the program VMD. I manipulated the backbond as cartoons, and then selected the histidine residues for display as CPK, and added some bonds to serve as supports to hold the structure together (these are the larger braces). This was then imported in several segments into tinkercad (tinkercad had a problem importing files larger than 20 Mb, so I had to import and then align as three components. I then grouped and aligned everything, and added a number of manual support features at the bottom. The smaller braces are designed to be removed, while the larger braces hold the model together.
If you do choose to print this out, be prepared for a significant level of work, but the print is very nice.

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This is simply awesome. Dunno about scientific usefulness, but to be able to hold the model of a protein in your hands is just so cool.

Yes, this is more of an academic effort than something of any particular utility. I plan to use it for teaching purposes. It is an ideal 4 alpha helical bundle that crystallized as a dimer. I think there is a certain amount of usefulness to being able to hold something in your hands for visualization. This is something you just can't get, even with some very nice 3D viewers out there. My next effort will utilize surfaces and a substrate cavity, which will hopefully be an easier print, and might assist in lessons about enzyme catalysis.

It's a great teaching effort, but I fear the sheer joy of it may be lost on anyone that doesn't really have a background knowledge of this stuff. Something akin to organic chem model sticks/balls when you first start playing with them. I wish you the absolute best and hope you produce a full working ribozyme that....interacts with...plastic...maybe...