Annual Scientific Report 2015

Protein Data Bank in Europe
The Protein Data Bank in Europe (PDBe) is an integrated structural data
resource that aims to evolve with the science of structural biology to serve the
needs of biologists.
PDBe handles the deposition and annotation of threedimensional
(3D) structural data, provides integrated,
high-quality macromolecular and (sub-)cellular
structures and related data and maintains in-house
expertise in X-ray crystallography, Nuclear Magnetic
Resonance (NMR) spectroscopy and 3D cryo-Electron
Microscopy (3DEM). We provide advanced services,
integrate structural and other information, and deliver
ligand-related, validation and experimental data.
Our mission is to bring structure to biology, and our goal
is to make PDBe the logical first stop on any quest for
information about 3D molecular and cellular structure.
Major achievements
The main highlight of 2015 for PDBe was the April
launch of the redesigned website (http://pdbe.
org). Several years of usability research, designing,
implementing, testing and incorporating userexperience
feedback culminated in a new website that
raises the standard for the delivery of 3D structural
information. The design of the website is in line with
the style of the main EMBL-EBI website. In addition,
we redesigned the individual pages for PDB and
EMDB entries from the bottom up, which resulted in
an intuitive layout and organisation, new categories
of value-added information (e.g. citation information
from Europe PMC and validation information based
on the wwPDB validation files), and a rich palette of
informative images. We also released a new, powerful
search system, which benefitted from input from
our BBSRC-funded BioSolr project. To provide
programmatic access to all our data, we developed an
application-programming interface (API) that supports
our new entry pages and can be used freely by external
software developers. Further details on the redesign
are described in this report by the PDBe Content and
Integration team.
The international wwPDB partners have been working
for several years to develop a joint, integrated software
system for deposition and annotation of structural data
from X-ray, neutron and electron diffraction, NMR and
3DEM. The new system (D&A 2.0), launched in January
2016, handles data to be deposited in the PDB, EMDB
and BMRB archives. In addition to improved integration
of data archiving for a variety of experimental
techniques, appropriate validation reports have been
developed for all relevant techniques. These reports are
produced by validation-software pipelines, which have
implemented recommendations from community-led
Validation Task Forces (VTFs), convened by wwPDB.
In 2015, our team put considerable efforts into the
final development and testing of D&A 2.0 before its
public release.
Since early 2015, PDBe has handled all D&A depositions
to the PDB from European laboratories and companies,
as well as all depositions that come through previous
deposition systems. The PDBe annotation team also
handles a substantial number of additional tasks,
including D&A testing, outreach (including social
media) and training. The number of PDB depositions our
highly skilled annotators processed in 2015 (4007 of 10
886 total worldwide, ~37%) is approximately double the
number we handled in 2013, both in absolute numbers
and in share of the worldwide depositions. In the same
period, they annotated 452 EMDB entries (~58% of
the worldwide total). Despite this high workload, we
processed over 90% of all depositions at PDBe within
48 hours.
Electron Microscopy
2015 was a very significant year for the field of 3DEM.
More laboratories and national facilities gained
access to state-of-the-art microscopes and detectors,
which generate datasets that require processing
using advanced software to optimize their utility. As a
result, high-resolution structures (i.e. better than ~4Å
resolution) started to be published so regularly that the
change was dubbed “the resolution revolution”. A record
resolution of 2.2Å was set in 2015, for a map and model
of β-galactosidase, both of which were deposited and
annotated at PDBe (PDB entry 5a1a and EMDB entry
EMD-2984). The journal Nature Methods named 3DEM
its “method of the year”.
PDBe is well positioned to support the 3DEM
user communities during this phase of very rapid
development, both as a founding member of the wwPDB
(where 3DEM molecular models are archived) and
as the birthplace of EMDB, where 3DEM maps and
tomograms are archived (EMDB passed the milestone of
3,000 entries in 2015). Moreover, in 2014 PDBe started
a new archive called EMPIAR, which serves as an
archive for raw image data (mostly related to structures
in EMDB). As the field expands and matures, the wide
availability of such data is very useful to spur software
and methods development, testing new approaches to
validation, distributing data related to controversial
studies, distributing data for community challenges
107
2015 EMBL-EBI Annual Scientific Report