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iCn3D Skill: Creating and Saving Selections

Last updated

Jan 9, 2025
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- iCn3D Skill: Analysis of Noncovalent Interactions
- iCn3D Skill: Mutations

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Structure

PDB ID: 3UBB
Protein: Rhomboid intramembrane serine protease GlpG (3UBB) with phosphonofluoridate inhibitor
Activity: Integral membrane serine protease
Description: Single chain transmembrane protease from E. coli bound to a phosphonofluoridate inhibitor, which is covalently bonded to the catalytic serine. Red and blue dots (“dummy” atoms) indicate extracellular and intracellular membranes, respectively. Uses a catalytic dyad composed of serine (S201) and histidine (H254).

Load Structure

Open iCn3D - https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
In the Please input MMDB or PDB, enter 3UBB. Press enter or click load biological unit.

Selecting using: 1. The structure viewer window with the Mouse and 2. The sequences and annotations menu (Key Learning Objectives)

This section will show how you can select residues, chains, etc in the Modeling window.

Select, Select on 3D to ensure default is Residue; With cursor, hover over the inhibitor (name 3UB) and Alt Click (option click on Mac) it. A yellow halo will appear around it.
Select, Save Selection, name it Inhibitor.
Now, use the top menu to open the sequences and annotations tab: Analysis, Seq. and Annotations
In the sequences and annotations window, uncheck “Conserved Domains,” and then click the Details tab. Click individually on the one letter code for S201 and H254. On selection, they will turn yellow.

(Note: To see the scroll bar in sequences/annotations in a Mac, choose Systems preferences in your operating system [not the iCn3D settings], General, show scroll bars and check always; see iCn3D About notes).

Select, Save Selection, name CatDyad

Rendering (Optional, can use the highlighted link below instead)

Select, defined sets (Note that “defined sets” brings up a complete list of objects, many selections are pre-built into iCn3D to get you started with a model.)
In Selected Sets, click 3UBB_A.
Color, Unicolor, Gray, Light Gray
In Selected Sets, click CatDyad
We want to show the side chain of the catalytic dyad, so use the top menu: Style, SideChains, Sticks
Recolor to CPK coloring: Color, Atom
Analysis, Label, Per Residue and Number
Analysis, Label Scale, pick number that works for you
Style, Background, Transparent
Remove any active selections (yellow glow) by Select, Toggle highlight

Pre-Rendered Model Link

https://structure.ncbi.nlm.nih.gov/icn3d/share.html?fhT3dwckYg8i5XJj8

The short URL above may be used to catch up for the next section of the tutorial

Selecting sphere within around 5Å of the inhibitor (Key Learning Objective)

Our goal is to find all atoms with 5Å from the inhibitor, this time without showing interactions. In the next step, we will designate 2 sets of objects. Set 1 will be the inhibitor. Set 2 will be nearby residues/bound molecules. In our case, Set 2 will be defined as the protein.

Select, by Distance
For the first set, select inhibitor; for Set 2 click 3UBB
For Set 2. Sphere with a radius to 5 Å
Click Display; Close the Select by distance window
Now save the highlighted groups 5Å from the inhibitor through Select, Save Selection, Name 5AfromInhib
Style, Side chains, Stick
Color, Atom
Select both the inhibitor and the surrounding residues: In Defined Sets, Click Inhibitor, and Ctrl+Click 5AfromInhib (Command+Click on a Mac)
Display only the active site for clarity: View, View Selection
Analysis, Label, Per Residue & Number
To see water, Style, Water, Sphere
File, Share Link, copy short link

Pre-Rendered Model Link

To check your work (or if you got stuck during any of the steps above) view the model using this link: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?sqZf4Zvqn5zWK21d9 This link shows the membrane. Choose View, Toggle Membrane to hide it.

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