About NCBI Structure

[We are starting in the Protein Database and we will link to Structure in this exercise.]

From nucleotide sequences we can determine possible amino acid sequences, and from amino acid sequences we can predict some elements of protein secondary structure (like alpha helices). However, it is currently not possible to reliably predict the three-dimensional structure of a protein just from the amino acid sequence. We therefore rely on techniques like x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to discover the 3D structure of proteins, and we use that data to make deductions about the structure of proteins that have similar amino acid sequences.

The NCBI Structure database contains protein information from crytallography and spectroscopy, including 3-dimensional renderings of protein structure, with information about the structure's molecular components.

To explore protein structures it is often useful to first identify the protein(s) of interest using the Protein database and then link to the Structure database from the protein record. Let's do this.

Search for a Protein

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Our goal is to explore the structure of a protein called HFE. This protein is involved in a condition called hemochromatosis

First find records for the HFE protein in humans using the Protein database.

hfe[ti] AND human[orgn]

Search: hfe[ti] AND humans[orgn]

[Note: If we wanted to look at the sequence of amino acids that make up this protein, we'd probably just use the Gene Sensor at the top of the results for a simple search (like HFE) to quickly go to the NCBI reference sequences (RefSeqs) for this protein. But we want to look at the structure, so we don't want to limit our search to RefSeqs.]

We know that the Protein Databank (PDB) is a good source for protein structures, so use the Source databases limit to restrict to only PDB records.

protein source databases

Search for a Protein

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Take a moment to look through these results. We're looking at records from the Protein Databank (PDB) for HFE proteins.

Look at the Accession numbers and the record titles. Note that each of these 4 records actually represent a chain from the same structure:

  • From a record with accession number 1A6Z, there are records for chains A through D.
four chains from same structure

Link from Protein to Structure

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Use the Find related data options on the right side of your screen to select the Structure database with the option "Structures."

Find related data

Link from Protein to Structure

2 of 2Using the Find related data from the Protein to the Structure database opens all of the structures in the Structure database that produce the chains represented by the results in the Protein database.

You should see one structure, with the familiar accession number (1A6Z).

1A6Z record

 

View a Structure

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Note the following components of a Structure Summary record:

experimental method

  • Experimental Method: This tells you how they determined the protein structure. This example was obtained by x-ray diffraction.
  • Resolution: Tells you the scale or resolution (in Angstroms) of a protein structure resolved by diffraction or electron microscopy.

biological unit graphic

  • Molecular Graphic: The rendering of the 3-D structure.
  • Interactions: A schematic of the protein chains and other, non-protein parts of the structure (small molecules).

molecular components

  • Molecular Components: A table listing all of the components of the structure, referring back to the schematic to show you where they are.

    [Note that - while it isn't the case in this particular record - some of the components of a structure in the Structure database may not be associated with the protein in nature -- they were necessary to be able to crystallize the structure to learn about it.]

View a Structure

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You can get a quick three-dimensional view of the structure using the link in the lower left, labeled "3D view".

To display the structure in the interactive viewer (called iCn3D), use the launcher that appears in the lower right of the molecular graphic ("full-featured 3D viewer").

Click "full-featured 3D viewer," now. (Use this link to open within the tutorial.)

3D options

View a Structure

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The iCn3D default display shows a ribbon-style abstract rendering of the alpha carbon backbone of the protein (without side chains). See Help for iCn3D.

"Grab" this structure with your mouse and move it around.

  • Zoom in using your mouse scroll wheel or <z> on your keyboard
  • Hold <Alt> and click to highlight sections of the structure; This will highlight in the rendering and also in the amino acid (residue) sequence shown in right panel.
  • Use the "Style" menu at the top to change how the parts of the structure look. 
  • Use the "Color" menu to color secondary structure, or color by atom.
  • Use the right pane to view important residues.

View a Structure

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You have reached the end of this tutorial on viewing a protein structure.

Continue to Chapter 9. Using PubChem to Find Structures With Specific Molecules

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