 Hi everyone, welcome to basic sign series. I'm your host Lokinder Kumar and today I'm going to make a video on protein and data bank Before we start using pi mole because this series will be everything We will know everything about pi mole that in this series I'm going to make videos on how to use pi mole how to make Publication quality figures in pi mole how to understand ligand interactions how to label amino acids in pi mole But before that we need to understand Protein and data bank first. So as you can see on your computer screen. So this is How protein data bank homepage look like there is a search tab here? so Here you can search the protein of interest that you want to work on and There are various other features I will not go into the detail of this particular homepage But I will go into the detail of the proteins Structural information about the proteins and functional information about the protein So let's start the tutorial by entering the name of the protein. For example I want to download the structure of a protein last are So see Domino surgeon osa is the name of the organism and last are is the name of the protein So you can also type last are directly So let me type last are and it's going to give you a lot of information. So you can also select From from these particular options that are available. For example, if I select the first Particular option that was given to me and now I can see these are the Structures that are available for that particular protein So this is very important point that for one particular protein you can you can get multiple structures So it depends upon The The type of the structures that you want to use for example many proteins have multi-domains So you can get various Various different different domains as a separate PDB structure You can get various conformation of the protein as a separate PDB structure So that depends upon your requirement. So you will get a lot of different different output results but I am interested in a particular Particular crystal structure and and for that I know the code. So this is Basically the code for that particular crystal structure. It's a four-letter code and when you start working on particular protein you need to remember this particular code so that you can mention that code in your research article and You should always work on that particular Particular code so that because the information will be very specific for your For your crystal structure. All right, so the code for my protein is Do you we zero? So I'm tapping to you be zero. So that's the Code for my particular protein Which is last freedom in our series, you know, so last are ligand and binding domain Okay, so let's see what kind of information We actually got from this particular search result. You can see it gives you the the four letter specific unique four letter code Then it gives you the the name of the protein, right? It gives you the structure of pseudomonas aeruginosa bound with auto inducer so auto inducer is the ligand present inside the protein and There are also Additional information for example, it gives you the name of the organism as already mentioned By me that the organism is pseudomonas aeruginosa and what is PA o1 PA o1 is the name of the strain Now you have expression system Expression system means the Organism that was used to purify that particular protein in this case you have E. Coli BL 21 as an expression system classification is another important parameter that I missed that classification tells you that What is the main function of this particular protein? So it is a signaling protein that is Responsible for the transcription of its genes so transcription is the main classification area then you get Important information about the crystal structure here. You can see the resolution 1.80 and our values information Then you have further the article information and The author information and you can also search this particular article by clicking on this particular link so you get most of the information about this structure on the on the structure summary page and Now let's move on to the second tab, which is 3d view in 3d view So it's more like pi mole Pi mole, but It doesn't give you a lot of a lot of control over over various things So that is why we use separate software for analysis, but it is also really good molecular graphic system and you can get a lot of information extracted from this particular 3d viewer of the PDB. So I'm gonna make this window much bigger and I'm gonna explain you what are these are these things. These are the sequences These are the name of the amino acids one letter code of amino acid and as you can see When I click on this one I get information here on the lower right corner of my screen about the amino acid So you can see while I'm moving I can get an information. So which is pretty convenient now I'm seeing four Domains so you can see four different colors. So they are four domains of the protein But in this particular protein The protein was purified as tetramer. So all the domains basically are same and What what what are the options that are available for you? you can see on the right side that you can show water molecules these red drop these small spheres are the water molecule if I click on this one and then the water molecules are No longer available in the crystal structure, then you have Ligand if I want to hide the ligand Now you can see that there is a difference But I can show you by hiding the overall structure of the protein now you can see if I hide everything And then one by one I can show you you can see ligands. So these are the ligands present in the In the protein structure, then I can show you the polymer and now you can see the polymer Which is protein or polypeptide in this case? So This is a 3d viewer and it gives you a good idea about the three dimensional structure of the protein If you are not using pie mold and you want to have a quick view of the 3d structure of protein It can have other options. You can also export the image by clicking on this particular Dab here, which is a kind of a shutter icon here, right? So you can also have some of the settings So you can change the background if I want to change the background to green or blue or dark black or Or some other colors, but white is the best option for one three figures. You can also change the Finishing you can see this is more metallic finishing. So your structure will look more Beautiful and catchy when you use these different different settings But anyways, one of the important thing that we're going to use In pie mold also is clipping clipping Cleaves the part of the protein and then you can no longer see that particular section of the protein So this is You can you if you can see that Some of the part of the protein is no longer is Available because I clipped that part of the protein, but anyways, we're gonna use those particular settings in the pie mold. So after Understanding the 3d viewer of PDB. Let's move on to the annotations Annotations so you'll get gene annotations protein annotations from this particular web page and They they are all the links that you can click and get the information about the annotations Then the sequence. It's really important Sequence you can get the faster faster file sequence Of that particular protein if you click on faster sequence, you will immediately download a faster file I'll show you how it looked like so it will look like the the alphabetical order of the amino acids in the protein sequence so that's the faster sequence of the protein and as you can see this is also very very informative Figure you can see in this case. It's a two-dimensional Structural information of the protein where you can see these are the alpha helix so this is also very useful information about the structure of the protein and Then the last step is the experiment experiment tab provides you all the details that would use to purify the protein Also to perform the crystal structural analysis, you can see during diffraction. What are the parameters that were used? And you can see during the crystallization experiment. What are the parameters that were used? So if you are trying to purify this protein and trying to do Structural analysis of this protein this page is really really helpful for you Alright, so if I go back to the home page on the home page You can see it provides the general information about the latest structures that are available in the PDB it also provides the molecule of the month in this case you can see it's a spike protein and And You can also see various other Additional tools that PDB provides. This is PDB 101 webpage of the protein data website which provides you exciting things for example various things for high school students so that they can Get attracted towards this this kind of research So there are various tools that you can you can explore in this particular website So lastly, we are going to know how to download the file and we are going to use that file for the PiMole sessions. Okay, so you can you can see this is the tab This is the most important tab that you're gonna use Frequently if you're using PiMole and if I click on this tab I can download faster sequence that I've already shown you the PDB protein data bank format which is the three-dimensional coordinates of the atoms and This is the format that we want to download to understand the functioning of PiMole, so I'm gonna click on this one and Immediately after clicking I will see a file is getting downloaded and this file The name of the file is the name of the four-letter code of the particular protein if I click on this one and You are going to see PiMole window open immediately on your computer and you can see this is the default view of the protein and From here, I'm going to start the PiMole tutorials So I'm going to show you how to make Structures, what are the different components that you're seeing right now on your computer screen and what are the functions of all those? components, so Stay tuned till I present you the next next video where I'm going to show you all those interesting Functions of PiMole and if you like the video, please press the like button and I'll see you in the next video