BIN-PDB

The RCSB-PDB Structure Database

(The RCSB PDB database and services)

Abstract:

This unit provides a short introduction to the PDB.

Objectives:
This unit will ...

... introduce the PDB and explore its use.

Outcomes:
After working through this unit you ...

... can navigate and use the PDB.

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Prerequisites:
This unit builds on material covered in the following prerequisite units:

[ PubMed ] [ DOI ] The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

Costanzo et al. (2016) Using the Tools and Resources of the RCSB Protein Data Bank. Curr Protoc Bioinformatics 55:1.9.1-1.9.35. (pmid: 27603019)

[ PubMed ] [ DOI ] The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc.

The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started.

Task:

Visit the RCSB PDB website at http://www.rcsb.org/pdb
Briefly orient yourself regarding the database contents and its information offerings and services.
Enter Mbp1 into the search field.
In your journal, note down the PDB IDs for the three Saccharomyces cerevisiae Mbp1 transcription factor structures your search has retrieved.
Click on 1BM8 entry and explore the information and services linked from that page.
- On the Structure Summary tab, note that this structure has 1.71Å resolution - which is very high. The protein feature view shows where the domain is located in the full-length protein. This page has a download link, from which you can get the PDB coordinates file, as well as the biological assembly (whenver that is relevant).
- On the 3D View tab, explore the visualization options. Set Style to "Licorice" to view individual bonds; set Color(sp.) "By Hydrophobicity" to see how hydrophobic amino acids define the core of the folded protein.
- On the Annotations tab, explore the cross-references. Pursue the link to the "Mlu1-box Binding Protein; DNA-binding Domain" annotation of the CATH database domain annotations at the Topology level, to see how many proteins with a similar fold are held in the PDB.
- Explore the other tabs, and take special note of the Structure Similarity tab. This is one of the important resources, the ability to find and superimpose similar structures helps tremendously in interpreting e.g. conservation patterns in a protein.

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