What's New in this Release (April 19, 2011)

 
Table of Contents:
 
  PDB-101: Educational Resources for Exploring a Structural View of Biology
  Structure Summary Sequence Tab
  Advanced Search
  Tabular Reports
  External Links
 
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PDB-101: Educational Resources for Exploring a Structural View of Biology
 
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PDB-101 is a new and unique view of the RCSB PDB that places educational materials front and center. It packages together the resources of interest to teachers, students, and the general public--Structural View of Biology, Educational Resources, Molecule of the Month, and Understanding PDB Data--to promote exploration in the world of proteins and nucleic acids.

Clicking on the blackboard PDB-101 logo or its related widget in the left-hand menu reveals an education-centered website. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the PDB-101 pulldown to jump to other sections of PDB-101. Click on the blue logo in the top left at any time to access RCSB PDB deposition and query services from the main website.

View PDB-101 Page

 

This initial release of PDB-101 offers:

  • Structural View of Biology. Built around the Molecule of the Month series, this feature promotes a top-down exploration of the PDB. Beginning with high-level functional categories, readers can browse through descriptive subcategories to access relevant articles that describe molecules in simple terms and access the related PDB entries. Mouseovers, pulldown menus, and carousels all offer easy navigational tools to promote learning.

  • Molecule of the Month series. Since 2000, the RCSB PDB has published articles that describe the structure and function of a molecule along with interactive views, discussion topics, and links to structure examples. The collection of these articles provides a annotated view of the PDB archive. With PDB-101, all Molecules of the Month appear on single pages, with links to printable PDF versions and downloadable high resolution images. They can be accessed through the pulldown menu in the top bar, the Structural View of Biology, and by archives organized by title, date, and category.

  • Related Educational Resources and materials, including posters, animations, and classroom lessons and activities.

  • Understanding PDB Data, a reference to help explore and interpret individual PDB entries. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges to exploring the archive.

PDB-101 will continue to be developed; we welcome your comments and suggestions.

To link directly to this view, use http://www.pdb.org/pdb-101.

 
 
 
 
Structure Summary Sequence Tab
 

The layout and navigation of the sequence page has been improved. Each macromolecule chain can be annotated with domain assignments, secondary structure, and structural features such as SNPs (Single Nucleotide Polymorphism), sites defined in the structure entry (i.e., binding sites of ligands) and protein modifications (i.e., posttranslational modifications). The annotations available vary for each structure. This page has been enhanced with:

 

Improved Layout

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The page is divided into the top right Sequence & Structure Relationships widget, and widgets that display the sequence and annotations for each chain. To view these annotations in 3D, launch the Jmol viewer and select an annotation to be mapped onto the structure.

Using the Display Parameters box, users can toggle between the display of unique chains and all chains. By default, only unique chains are displayed. This box can also toggle the display of the UniProtKB reference sequence.

View sequence page for hemoglobin (4HHB)

 
 
 

Single Nucleotide Polymorphism (SNP)

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SNP annotations can be added to the sequence diagram using the Add Annotations pulldown menu. SNPs will appear as small circles in the diagram; mousing over the SNP circle will display related information. Click on the SNP circle to map it onto the Jmol 3D display. SNP data, provided by the LS-SNP database, are also available in tabular form on the Biology and Chemistry tab.

View sequence page for EGFR kinase domain (2EB2). Add the SNP annotation to display the location of four SNPs in the sequence diagram.

 
 
 

Binding Sites

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PDB entries may contain records that indicate important sites such as ligand binding sites. Site records have been generated by the entry author and/or by software based on a distance cutoff from a ligand. Select Structure Feature>Site Record from the Add Annotations pulldown menu to include site records in the sequence diagram as circles. Then select Display Jmol to map the site records on the 3D structure. Jmol displays these residues as stick figures, and the bound ligand as ball & stick.

View sequence tab for streptavidin complex with biotin (1STP). Add the Site Record annotation to display the location of the biotin binding site in the sequence diagram.

 
 
 

Protein Modifications

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Protein modifications represent pre-, co-, or post-translational modifications. More than 200 types of protein modifications have been collected from the RESID database, PSI-MOD protein modification ontology, and the wwPDB Chemical Components Dictionary, and mapped to PDB sequences. Select Structure Feature>Protein Modification from the Add Annotations pulldown menu to add these annotations to the sequence diagram.

In the sequence diagram, the shape of the symbol indicates the number of residues involved in the cross-link as defined in the legend. The image shown here displays a modification with an iron-sulfur cluster 4Fe-4S. In this case, the rhombus represents a cross-link 4, with four cysteins involved in the metal complex. Map this modification onto the 3D structure by clicking on the feature in the sequence diagram.

View sequence page for ferredoxin (1B0V). Add the Protein Modification annotation to see the location of the modified residues in the sequence diagram.

The list of protein modifications will be expanded in the future.

 
 
 
 
 
Advanced Search
 

Protein Modifications

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The protein modifications described in the previous section can be searched from the Advanced Search interface.

Two pulldown menus can be used to specify the protein modification source type (all sources, RESID, PSI-MOD, and Chemical Component Dictionary) and the associated name/ID of the modification.

The image on the left shows an example search for 4Fe-4S iron sulfur clusters by name tetrakis-L-cysteinyl tetrairon tetrasulfide. The protein modification details can be viewed on the Sequence tab (see previous section).

View PDB entries with tetrakis-L-cysteinyl tetrairon (RESID AA0140) modification

 
 
 

Pfam ID Search

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A search by Pfam IDs has been added to the advanced search. The Pfam Database (Pfam) provides a classification of proteins into families and domains using hidden Markov models.

View PDB entries for Pfam family PF00104 (nuclear receptors)

 
 
 

Finding EM Structures with Experimental Data Files

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Use Advanced Search to find structures determined by electron microscopy for which experimental data files are available in the PDB or at the Electron Microscopy Database (EMDB). In most cases, experimental data for EM structures are electron density maps, but a few EM structures have structure factor files or both types of experimental data (e.g., 3EPC).

To find all EM structures with experimental data select "Experimental Methods" from the "Methods" section of the Advanced Search pulldown menu. Then select "ELECTRON MICROSCOPY" from the "Experimental Method" and choose "Yes" from the "Has Experimental Data" pulldown menu.

View electron microscopy entries with experimental data

 
 
 
 
Tabular Reports
 

EM Tabular Reports

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A new experimental report section for EM has been added in the "Generate Reports" menu. Generate an EM Structure summary report by selecting "EM Structure" in this section.

By default, the EM Structure Report includes PDB ID, EMDB ID, Exp. Method, Resolution, Aggregation State, Symmetry Type, Reconstruction Method, Specimen Type, Release Date, and Deposition Date. These fields can also be included in a customized report.

View an EM Structure summary report example.

 
 
 

New Custom Tabular Report Fields

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In addition to the new EM Structure fields (image above), two other new fields are options for the Custom Tabular Reports: Last Page (in Primary Citation) and Taxonomy ID (in Biological Details).

 
 
 

Tabular Report Web Services

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Generating tabular reports programatically using RESTful Web Services. By passing in PDB IDs and field names as arguments, any predefined or custom report can be created. For example:

http://www.pdb.org/pdb/rest/customReport?pdbids=1stp,2jef,1cdg& customReportColumns=structureId,structureTitle,resolution& service=wsfile&format=csv will launch a download of a report that contains Structure ID, Structure Title, Resolution for PDB IDs 1stp, 2jef, and 1cdg.

Visit the guide to Custom Report Web Services to start to use this feature. An example (in Java) is available.

 
 
 
 
External Links
 
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The Advanced Search option for "Has External Links" finds entries that have links to information from other sources. This feature now includes the HIV Toolbox, a resource that provides sequence, structure, and function annotation and visualization of more than 600 HIV protein structures, developed by the Martin Schiller lab at the University of Nevada Las Vegas.

Links to the HIV Toolbox are found in the Links tab (under Structure Features) for corresponding PDB entries.

View the Links tab for HIV-1 reverse transcriptase (3FFI)