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Merged PDB split files: View large macromolecules in their entirety

[25 JUL 2012]  It is now possible to interactively view and/or download large macromolecular structures in their entirety, such as the viral capsid illustrated below, the rat liver vault, and the ribosome structure by Nobel Laureate V. Ramakrishnan, and more. These and approximately 150 other large macromolecular structures exceed the size limits implicit to the PDB file format and are therefore split into several PDB files. The MMDB data processing procedure merges the files into a single structure record, and the merged files can be viewed interactively with Cn3D 4.3 (install). You can also retrieve all merged files, if desired.


 
PDB SPLIT FILES for the
Adeno-associated Virus Serotype 6 (Aav-6)		 right arrow MMDB MERGED FILE
PDB ID: 1VU0 PDB ID: 1VU1 PDB ID: 3TSX right arrow MMDB ID: 99554
First of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 1VU0. Second of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 1VU1 Last of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 3TSX. right arrow The MMDB record for the Adeno-associated Virus Serotype 6 (Aav-6), in which the data from the three PDB split files have been merged together to provide a 3D view of the complete structure, shown here in MMDB ID 99554. The entire structure and its sequence data can be viewed interactively in Cn3D.
Click on the thumbnail image above to open the merged file in Cn3D 4.3 and interactively view the entire structure and its sequence data.
 
 
 
Database Statistics
 

As of 18 September 2012:

84,199 structure records total
 

21,207 protein only
     703 DNA only
     488 RNA only
 

56,739 protein bound to chemicals
     709 DNA bound to chemicals
     464 RNA bound to chemicals
 

  2,371 protein-DNA complexes
  1,030 protein-RNA complexes
     103 protein-DNA-RNA complexes
       38 DNA-RNA complexes
 

(see how to create these queries...)


 
News Archive
 
 

Entrez Structure interface redesign

[25 JULY 2011]  NCBI's Structure database now has a revised home page, search interface, and search results display, to have functions similar to those available in PubMed. Changes include: (a) a streamlined home page with links to related resources; (b) an "Advanced Search" page, which provides the ability to build a query one term at a time, browse the index of any search field, and combine earlier searches; and (c) new search results displays that provide links in the right margin to search filters, related data, and tools.

 

Cn3D 4.3 now available

[25 MAY 2011]  A new version of NCBI's macromolecular structure viewing program, Cn3D 4.3, is now available (download). New features include the ability to view biological unit(s), including those containing molecules generated by applying transformations from crystallographic symmetry, side by side stereo views, additional alignment algorithms for editing multiple sequence alignments, new highlighting features, and more. It is similar to the Cn3D 4.2 preview release that was packaged with CDTree, but has been packaged as a standalone program and enhanced to handle the new Molecular Modeling Database (MMDB) data specification that now includes biological units and interactions.

 

New structure summary pages featuring biological units and interactions

[09 MAY 2011]  MMDB structure summary pages have been revised to display salient features of each structure, including its biological unit(s) and an interaction schematic depicting the interactions among the structure's molecular components, as in the human hemoglobin example below. The procedures to identify a structure's biological unit(s) and thresholds used to display interactions are described in the help document.


 
ASYMMETRIC UNIT (RAW DATA) IN THREE DIFFERENT STRUCTURE RECORDS FOR HUMAN HEMOGLOBIN: right arrow BIOLOGICAL UNIT
IS SIMILAR IN ALL
PDB ID: 2DN2
MMDB ID: 39206		 PDB ID: 1LFT
MMDB ID: 20898		 PDB ID: 1LFL
MMDB ID: 20896		 right arrow MMDB summary page displays the biological unit by default:
3D view of the raw data for human hemoglobin submitted in PDB record 2DN2, which contains a complete copy of the structure's biological unit (in this case, a tetramer). Click on the thumbnail to open the structure record in MMDB, where you can launch an interactive 3D view and then color by molecule, as shown here. 3D view of the raw data for human hemoglobin submitted in PDB record 1LFT, which contains half of the structure's biological unit (that is, half of the hemoglobin tetramer). Click on the thumbnail to open the asymmetric unit view in MMDB, where you can choose to view the biological unit and/or launch an interactive 3D view, and then color by molecule as shown here. 3D view of the raw data for human hemoglobin submitted in PDB record 1LFL, which contains two copies of the structure's biological unit. Click on the thumbnail to open the asymmetric unit view in MMDB, where you can choose to view the biological unit and/or launch an interactive 3D view, and then color by molecule as shown here. 3D view of the biological unit (tetramer) of human hemoglobin. To view it interactively, click on any thumbnail to the left to open the structure's record in MMDB, select the biological unit display option, then launch the interactive 3D view and color by molecule, as shown here.
Complete tetramer of human hemoglobin Half of the tetramer, which can be used to reconstruct the complete tetramer by applying tranformations derived from crystallographic symmetry Two copies of the tetramer   and an interactions schematic:
Interaction schematic for the human hemoglobin tetramer, showing protein molecules as circles and heme groups as diamonds, with lines indicating interactions with at least 5 contacts a distance of 4 Å or less between the heavy atoms.
 
 
 
 

Cn3D 4.2 preview available

[09 MAY 2011]  A preview of a new version of NCBI's structure viewing program, Cn3D 4.2, is packaged together with the CDTree program (install). New features include:

  • the ability to view the biological units identified within a structure, including those containing molecules generated by applying transformations from crystallographic symmetry
  • side by side stereo views
  • additional alignment algorithms for editing multiple sequence alignments
  • new highlighting features
  • more robust handling of sequence identifiers
 

"Selected Structures" display in Entrez Structure search results

[03 JUN 2010]  When you search the Entrez Structure (Molecular Modeling Database) database, a "Selected Structures" summary box now appears in the upper right corner of the search results page (for example, see the results of a search for p53 tumor suppressor). The "Selected Structures" box lists the top five protein domain families found among the retrieved structures, inferring protein function, as well as the top five organisms represented in the structures. It also provides easy access to various subsets of structure records in the search results, such as those composed of specific molecule combinations (e.g., protein-protein, protein-DNA, protein-chemical), and those with links to literature in PubMed or free full text in PubMed Central.
 

Inferred Biomolecular Interactions Server (IBIS) publicly available

[18 AUG 2009]  The NCBI Inferred Biomolecular Interactions Server (IBIS) server was made public. For a given protein sequence or structure query, IBIS reports physical interactions observed in experimentally-determined structures for this protein. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation. (read more about IBIS; additional publications)
 
 
 
 
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