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Cytochrome C (Human) (PDB 1J3S)

by MoleculeMaker, published

Cytochrome C (Human) (PDB 1J3S) by MoleculeMaker Mar 24, 2013

Description

This is a model of the structure of human cytochrome C. The model is based on the solution structure and the PDB file 1J3S.

This printed well, and is now a completed model. I have painted it and provided some pictures.

This protein is the human version, and is important for the transfer of electrons in the electron transport chain. It has a single heme heteroatom, which I have represented as CPK, along with the histidine ligand. I was a little bit upset by how flimsy it was following the initial print, but actually have grown to like it very much, as it gives one the sense of the fluidity of the protein backbone and structure. It is not as sturdy as some of my other models, but turned out very nice.

Recent Comments

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I first work in the program VMD. In this program, I usually will split the file into several pieces. I also put a specific component (usually a single amino acid) in each stl file as I slowly import these into tinkercad. I just recently purchased a copy of camtasia, and plan to post some youtube videos soon to walk people through the process if they are interested. It is a little too detailed to try to explain how I do this here. If you send me an e-mail, I can send you some more detailed instructions on what I do.
Great model. I assume you imported the model into Tinkercad to add the supports, how were you able to split the model up for importing? Thanks for sharing your expertise.
Yeah, a little bit tedious to get into some of the spaces, but I think these are really enhanced by a little bit of color. Working on another model now that is primarily beta sheet (plastocyanin), and then I might try something really tricky.

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Instructions

This structure is an extensive print. THIS CAN ONLY BE PRINTED WITH SUPPORT selected in Makerware, and a word of warning, expect 2-3 hours to remove the support and get down to the actual model. I removed the supports as well, and have painted it. I am printing at medium quality. The build time was nearly 8 hours, so be warned, it takes some time. This model is somewhat fragile, so take your time removing the support. I use a pair of needlenose pliars to break off the support structure slowly, and remove the support from the remaining model. I printed this out on a Makerbot Replicator 2.

The model took a good deal of effort to construct. The original pdb file (1J3S) was manipulated until only the single monomer 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 ligand and heme for display as CPK, and added some bonds to serve as supports to hold the structure together (these are somewhat flimsy). 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. I did break a small section at the end of the molecule at one point, which I had to glue along with one of the supports for the heme. These glued well with standard model glue.

If you do choose to print this out, be prepared for a significant level of work, and be patient removing the supports, but the print is very nice. I painted the alpha helices in orange and the beta sheets in teal, and also painted the individual atoms of the heme and histidine ligand. The iron was painted green.
Great model. I assume you imported the model into Tinkercad to add the supports, how were you able to split the model up for importing? Thanks for sharing your expertise.
I first work in the program VMD. In this program, I usually will split the file into several pieces. I also put a specific component (usually a single amino acid) in each stl file as I slowly import these into tinkercad. I just recently purchased a copy of camtasia, and plan to post some youtube videos soon to walk people through the process if they are interested. It is a little too detailed to try to explain how I do this here. If you send me an e-mail, I can send you some more detailed instructions on what I do.
Very cool. I might try printing out one of your ribbon models at some point. The paint is what really makes it look amazing.
Yeah, a little bit tedious to get into some of the spaces, but I think these are really enhanced by a little bit of color. Working on another model now that is primarily beta sheet (plastocyanin), and then I might try something really tricky.
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