Nature Methods | VOL 15 | JUNE 2018 | 403–409 | www.nature.com/naturemethods
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The Sutter BOB – designed to eliminate the conventional microscope frame – is a versatile, open-design upright microscope
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Simple coarse height adjustment
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A home for integrative structural models
PDB-Dev hosts integrative structural models of biomolecular assemblies solved by hybrid methods.
he Protein Data Bank, or PDB, is
an essential resource for archiving,
validating and disseminating
biomolecular structure models to a broad
community. Currently over 135,000
structure models—determined by X-ray
crystallography, nuclear magnetic resonance
(NMR) spectroscopy and cryo-electron
microscopy (cryo-EM)—can be found
in the PDB.
Despite recent remarkable technological
advances for structure analysis, especially in
the field of cryo-EM, there are many large,
complex, dynamic biomolecular assemblies
that just cannot be solved with a single
structure-determination technique. To solve
these challenging structures, researchers
can apply ‘hybrid’ methods—including
lower-resolution approaches such as electron
tomography, small-angle X-ray scattering,
cross-linking–mass spectrometry and
others—to generate spatial restraints. These
spatial restraints provide key clues about the
arrangement of assembly subunits and are
applied in ‘integrative’ modeling pipelines
for structure determination.
The PDB, however, does not have the
infrastructure to handle models produced
via hybrid methods. With the development
of a prototype system, PDB-Dev, integrative
models now have a home.
Integrative models pose several
challenges for archiving. Such models
may contain multiple resolution scales or
conformational states, or may be represented
as ensembles of structures. PDB-Dev
was built on the existing data standard
for the PDB, ensuring interoperability
and extensibility. Besides the integrative
models themselves, PDB-Dev archives the
experimental spatial restraints, modeling
pipelines used and associated metadata.
At the moment, preliminary validation
metrics are available in PDB-Dev, but
further community input will be needed to
develop such metrics for integrative models.
PDB-Dev currently contains nine
integrative models and is open for new
submissions at https://pdb-dev.wwpdb.
org. The resource will surely have a positive
impact and facilitate greater reproducibility
and transparency in structural studies of
Published online: 31 May 2018
Vallat, B. et al. Development of a prototype system
for archiving integrative/hybrid structure models
of biological macromolecules. Structure https://doi.