Explore Integrative Structures at RCSB.org

05/28

RCSB.org now offers expanded access to integrative structures. Users can access explore these complex macromolecular assemblies modeled using integrative methods together with other experimental structures and Computed Structure Models using their favorite RCSB PDB tools.

What are Integrative Structures?

Integrative structures are determined using a combination of data from traditional techniques such as X-ray crystallography, NMR spectroscopy, and 3D Electron Microscopy (3DEM) along with other experimental approaches like Small Angle Scattering (SAS), Crosslinking Mass Spectrometry, Atomic Force Microscopy, Forster Resonance Energy Transfer, and more. These methods help build structure models of large, dynamic, and heterogeneous biological assemblies that are difficult to resolve with a single technique. Integrative structures are deposited and processed by the wwPDB through PDB-IHM (via OneDep) and archived alongside experimental structures in the PDB archive (see announcement). Well-known examples of macromolecular complexes modeled using integrative approaches include the nuclear pore complex, BBSome, and the nucleotide excision repair complex.

Searching and Exploring Integrative Structures at RCSB.org

RCSB.org offers multiple ways to find integrative structures:

Keyword or PDB ID searches in the top Basic Search (e.g., “BBSome” or “8ZZE”)
Advanced Search: Use the Integrative/Hybrid Method Details section to filter by model features (multi-scale, multi-state, ordered states), experimental input types, or related datasets in EMDB, BMRB, PRIDE, and more (Type "IHM" into the attribute box to highlight available options)
Results Refinement: After any search, filter results by Structure Determination Methodology>integrative

Integrative structures are marked with a distinctive puzzle piece icon, making them easy to identify at a glance in search results.

Structure Summary pages for integrative structures highlight key information about the representative model (see example.

Structure of the Nup84 sub-complex of the Nuclear Pore Complex. Visit the Structure Summary pages to access structure information.

Downloading IHM Data and Validation Reports

Integrative structures are only available in the PDBx/mmCIF file format in the PDB archive, and can be downloaded from Structure Summary Pages and the RCSB.org download tool. These data are not compatible with the legacy PDB file format.

The IHMCIF extension to the PDBx/mmCIF dictionary is the data standard used for macromolecular structures from integrative and hybrid modeling.

Full and summary validation reports in PDF format for integrative structures can also be accessed from Structure Summary pages.

A user guide offers detailed information on Integrative Structures at RCSB.org.