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NCBI Structures: Viewing a Protein Structure

This tutorial demonstrates how to find a protein in the NCBI Protein Database and view it in the NCBI Structure database.

Click Next to begin.

About Protein Structures

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 (3D) 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.

NCBI Structure Database

The NCBI Structure database contains protein information from crytallography and spectroscopy, including 3D 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.

Hemochromatosis is a disease in which too much iron builds up in your body. The HFE protein interacts with other proteins on the cell surface to detect the amount of iron in the body. In primary hemochromatosis, faulty HFE genes cause the body to absorb too much iron.

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

Search: hfe[ti] AND humans[orgn]

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.

Search for a Protein

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We’re now viewing the human protein records with "hfe" in the title of the record.

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

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 records represent a chain from the same structure:

  • From a record with accession number 1A6Z, there are records for chains A and C.

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."

Click Find items.

Link from Protein to Structure

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Using 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).

View a Structure

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Note the following components of a Structure Summary record:

  • Experimental Method: How they determined the protein structure. This example was obtained by x-ray diffraction.
  • Resolution: The scale or resolution (in Angstroms) of a protein structure resolved by diffraction or electron microscopy.
  • 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: A table listing all of the components of the structure, referring back to the schematic to show you where they are.

Note: 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.

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" (click and hold) this structure with your mouse and move it around.

  • Zoom in using your mouse scroll wheel or by pressing "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.

Conclusion

Congratulations! You are now able to find and view a protein structure using the NCBI Protein and Structure databases.

You may now close both Navigator windows.