2023

ANNUALREPORT

RCSB.ORG A LIVING DIGITALDATA RESOURCE THAT ENABLESSCIENTIFIC BREAKTHROUGHSDIRECTOR’S MESSAGE
The Research Collaboratory for Structural Bioinformatics
Protein Data Bank (RCSB PDB) works with community
stakeholders to preserve and deliver rigorously-validated,
expertly-biocurated, three-dimensional (3D) biostructure
information archived in the Protein Data Bank (hereafter
PDB or the archive) to many millions of PDB Depositorsand Data Consumers worldwide at no charge andwith no limitations on usage.
Exploration of these experimentallydetermined structures of proteins andnucleic acids (and their complexes
with one another and small-molecule
ligands) via RCSB PDB web portals is
enabled by state-of-the-art data analysis,
visualization, and download tools.

Stephen K. Burley, M.D., D.Phil.
Director
RCSB Protein Data Bank
University Professor and Henry
Rutgers Chair
Rutgers, The State University of
New Jersey
Research Scientist
San Diego Supercomputer Center

The PDB was established in 1971
as the first open-access digital data
resource in all of biology, founded on
bedrock values of open access andfacile reuse. The archive is an exemplarof the FAIR (Findability, Accessibility,
Interoperability, and Reusability) and FACT(FAIRness, Accuracy, Confidentiality, andTransparency) principles underpinningof responsible data stewardship. It isa vanguard in the open-access data
movement. Beginning with only sevenprotein structures, PDB holdings havegrown more than 30,000-fold.
Now in its 53rd year of continuous
operations, the PDB has global reach.
Approximately 60,000 structural biologists(Depositors) working on every inhabited
continent have contributed data to thearchive. This information is used bymany millions of PDB Data Consumers(basic and applied researchers, trainees,
educators, and students) based in >200
UN-recognized sovereign countries
and territories. The archive has been
designated by the Global Biodata Coalition
as a Global Core Biodata Resource,
and CoreTrustSeal-certified.
The PDB is managed by an international
collaboration among data centers,
called the Worldwide Protein Data Bank

2023 ANNUAL REPORT | PAGE 2(wwPDB). RCSB PDB is the global archive
keeper and the US data center in thiscollaboration. The estimated replacement
cost of current archival contents
exceeds US$20 billion.
PDB data are critical to public health.
Structural biologists and PDB data
contributed to design and rapid Emergency
Use Authorization of two highly-effectivemRNA vaccines against SARS-CoV-2, andto discovery and development of Pfizer’s
antiviral Paxlovid, saving many millionsof lives worldwide. RCSB PDB developed
many images, publications, videos andcurricula to help explain how the virus
works that were widely accessed
during the pandemic.
It is undeniable that the recentlydeveloped Artificial Intelligence (AI) andMachine Learning (ML)-based softwaretools for predicting protein structures fromamino acid sequence information alone(computed structure models, CSMs) would
not exist but for open access to PDB data.
In 2022, RCSB PDB further solidified its
position as the premier one-stop shop forstudying 3D structures of biomolecules byenhancing its research-focused web portal(RCSB.org) to support parallel delivery of
more than >1,000,000 CSMs of proteins
alongside >200,000 PDB structures,
enabling basic and applied researchacross the sciences.
Between 2019 and 2023, more than
67,000 atomic coordinate files and related
experimental data files were publicly
released. During the same five-year
period, PDB data files were accessedmore than 10.7 billion times from wwPDB
data centers around the world. During2023 alone, PDB data were accessedfrom RCSB PDB more than 2.6 billion
times. Additionally, 476 trusted external
information resources repackage anddistribute PDB data for the global scientificcommunity. PDB data are also maintained
as standalone copies of the archive inside
for-profit company firewalls.
RCSB.org supports an international
community of users, including biologists(in fields such as structural biology,
biochemistry, molecular and cellularbiology, genetics, pharmacology); otherscientists (in fields such as bioinformatics,
software developers for data analysis andvisualization); students and educators(all levels); media writers, illustrators,
textbook authors; and the general public.
Users access tools for searching, reporting,and visualization are integrated with a
database that contains data from the
PDB archive, data and links from external
resources, and pre-calculated data.
Searches range from quick queries (author
name, ID) to asking more complicatedbiological questions. For 2023, RCSB PDB
Usage Analytics recorded RCSB.org accessby ~8.2 million unique IP addresses making~3.5 billion requests/interactions (involving
delivery of >622 TB of data).
RCSB PDB also supports US research by
empowering a diverse STEM workforce
through Training activities, advancing
the frontiers of basic research anddiscovery through strategic initiatives(e.g., incorporating CSMs at RCSB.org),
and enabling applied research in academe
and industry with data and tools for

exploring new technologies (e.g., protein
engineering, de novo protein design,molecular nanotechnology). Training,
Outreach, and Education materials areavailable on the dedicated website
PDB-101 (“101”, as in an entry-levelcourse, PDB101.RCSB.org).
All feedback on RCSB PDB activities iswelcome at RCSB.org and at
info@rcsb.org.
Stephen K. Burley, M.D., D.Phil.

RCSB PDB SERVICES OVERVIEWIMPACT OF THE DATA AND SERVICESn SERVICE 0

IT INFRASTRUCTUREPDB Data

IT Infrastructure supports all RCSB PDB Services andsystems by establishing policies and processes toensure standardized systems configurations andmanagement, redundancy, security, highavailability, and disaster recovery.

• Enable research in subject areas from
Agriculture to Zoology• Contributed data to >1 million publishedresearch papers• Reused by 476 biological data resources

DATA DEPOSITION AND BIOCURATIONThe PDB Archive

RCSB PDB and other members of the Worldwide
PDB support tens of thousands of individual data
depositors around the globe, ensuring completenessand high quality for the ever-growing body ofexperimental structure information.

• Grows at the rate of nearly 10% per year
• Used to download ~5 million data files per day• Manages “Big Data” as a global Public Good• Provides data critical to AI/ML development
PDB Data Impact

ARCHIVE MANAGEMENT AND ACCESS• Basic and applied research• Patent applications• Discovery of life-changing drugs• Innovations that can lead to new productdevelopment and biotechnology
company formation• PDB-101 materials illustrate how PDB data help
explain fundamental biology, biomedicine, energy
sciences, and bioengineering/biotechnology• Training materials help our users make the mostof the PDB data and tools in researchand educationn SERVICE 1

n SERVICE 2RCSB PDB maintains the PDB archive according to
FAIR principles, provides FTP access to the data,and integrates the structural information withother scientific resources.

n SERVICE 3DATA EXPLORATIONRCSB PDB develops tools for searching, visualization,
and analysis of PDB structures and computed
structure models (CSMs). These tools arefreely available on RCSB.org.

n SERVICE 4
TRAINING, OUTREACH, AND EDUCATIONRCSB PDB creates resources to support the broaduser community in research, education, and training,
made freely available on PDB101.RCSB.org.

Economic Impact• The cost to replicate the contents of the
PDB archive is estimated at more than
US $20 billion• The PDB data and RCSB PDB services
generate annual Return on Investment ofmany thousand times federal funding
2023 ANNUAL REPORT | PAGE 3

DEPOSITION AND BIOCURATIONSERVICE 1

2023 HIGHLIGHTS

Supporting Data Depositors who freely contribute the resultsof their structural studies of biological macromolecules to the
PDB. All data deposited undergo expert review. Each structureis examined for self-consistency, standardized using controlled
vocabularies, cross-referenced with other biological data
resources, and validated for scientific/technical accuracy.
The Worldwide Protein
Data Bank (wwPDB)
was established in2003 to manage the single PDB archive of
macromolecular structural data and makeit freely and publicly available to the global
community. It consists of organizations thatact as deposition, data processing, anddistribution centers for PDB data.
PDB structures contain
•
•
•
•
•
•
•
•

3D atomic coordinates
Experimental data
Mandatory metadata
Authors (e.g., PI contact information)
Primary citation
Sample preparation, data collection,and structure determination details
Polymer sequence(s) (proteins, DNA,
RNA, oligosaccharides)
Chemical information

All deposited data undergo expert review
by Ph.D.-trained biocurators. Eachstructure is examined for self-consistency,
standardized using controlled vocabularies,
cross-referenced with other biological data
resources, and validated for scientific/
technical accuracy.
Validation is central to ensuring thehighest quality data. wwPDB Working
Groups and Task Forces include more than
100 academic and industrial volunteers
who develop data standards, makerecommendations, and contribute softwaretools used to generate wwPDB Validation
Reports that assess the quality andaccuracy of every structure stored in the
PDB archive. Servers and APIs are provided
for independent use by depositors prior to2023 ANNUAL REPORT | PAGE 4

17,063structures depositedand processed

3,623

new ligands created in theChemical Component Dictionary

30

data submission, and reports are provided
during biocuration.

new Biologically Interesting
Molecule Reference Dictionary
items created

wwPDB Validation Reports made available
once a structure deposition is complete
can be provided to journal editors andreviewers to help ensure the integrityof peer-reviewed scientific literature.
Validation data are also provided publicly
to enable meaningful analyses andcomparisons across the entire archive.

Open Access to SARS-CoV-2 structures
remains a high priority; 1,053 SARS-CoV-2
structures were deposited, rigorously
validated, expertly biocurated, andreleased in 2023; 3,913 were available
at the start of 2024.

In 2023, 17,063 new structures were
deposited and processed. 3,623 new small
molecule ligands and 30 new BiologicallyInteresting Molecule Reference dictionary
items were created. RCSB PDB is
responsible for managing depositions fromthe Americas and Oceania. Of the 6,697
US structures released in 2023, ~69%
reported NIH funding; ~11% reported
NSF funding. ~89% of X-ray structures
released in 2023 from US labs utilized
DOE-supported synchrotron or XFEL
facilities for data collection.

wwPDB regularly standardizes and updates
PDB data across the archive. In 2023,
updates included improved collection ofstarting models, standardized sequenceannotations for expression tags, crossreferencing XFEL structures with diffraction
images, translating atomic coordinates
to the standard crystal frame, andstandardizing restraint data formatting
for NMR structures. Additionally, peptide
residue chemical components were updatedwith standardized atom nomenclature andadded backbone annotation.

OneDep

wwPDB develops and uses the global OneDep system for data
deposition, validation, and biocuration. This single system helps tomaintain high data quality and completeness within the PDB archive,
while supporting growth in the number, size and complexity of thedeposited structures.
OneDep software is regularly updated to facilitate data submission. In
2023, deposition contact authors became able to utilize their ORCiDs
to access a summary table displaying all corresponding entries.
RCSB PDB

PDBe

PDBc

PDBj

Additional experimental method-specific data are collected by wwPDB partners
BioMagResBank (BMRB) and Electron Microscopy Data Bank (EMDB).

ARCHIVE MANAGEMENT AND ACCESSSERVICE 22023 HIGHLIGHTS

Supporting PDB Data Consumers by maintaining the PDB
archive, developing and standardizing the data dictionary,enabling global data delivery and DOI registration, andintegrating PDB data with other trusted information.

14,517new structures released
into the PDB archive

2.6 billion

Data dictionary terms and definitions
are formulated, reviewed, and modified
to support remediation of existing dataand inclusion of new and rapidly evolving
methodologies, from new experimental
techniques to Computed Structure Models.

Another milestone was reached this year.
Historically, identifiers for small ChemicalComponents like ligands have utilized
three characters. However, all available
three-character Chemical Component IDs
have been exhausted, leading wwPDB to
introduce five-character alphanumericaccession codes for new components.

PDBx/mmCIF also enabled development ofa “Next Generation” PDB Archive (NextGen,
files-nextgen.wwpdb.org) that offers
enriched annotation from external databaseresources such as UniProt, SCOP2, andPfam at atom, residue, and chain levels;and intra-molecular connectivity foreach residue present in an entry.

Late 2023 5 Digits CCD IDs

To support RCSB.org data delivery,
calculations are run weekly to generate
clusters of similar sequences and 3D
structures to support search and analysis
applications. Data are also integrated
with 50 trusted external data resourcesfrom across the Life Sciences information

ExamplesOn January 10, 2023, the PDB archive
surpassed the milestone of 200,000
structures. Throughout the year, a
record 14,517 new PDB structures werereleased, leading to year-end total holdingsof 214,121 available PDB entries.

A1LYA

A1D5A

data file downloads fromRCSB PDB-hosted FTP
and websites
ecosystem to provide the most complete
and up-to-date representation of a
PDB structure.
In 2023, 2.6 billion data files in various
file formats, including structure files,
experimental data files, chemical andmolecular reference data files, FASTA
sequence files, and validation reports, were
downloaded and/or viewed from RCSBPDB-hosted FTP and websites. Additional
data were downloaded from wwPDB
partners PDBe and PDBj, giving a wwPDBwide total of >3 billion data file downloads.
PDB data are also delivered through476 external resources that repackage andredistribute PDB information, and throughcopies of the archival data stored inside forprofit biopharmaceutical company firewalls.

Before 2023 3 Digits CCD IDs
ExamplesPDB ARCHIVE CONTENTS | December 31, 2023
U7C

V1X

In its role as wwPDB-designated archive
keeper, the RCSB PDB is responsible forsafeguarding and maintaining the archive.
RCSB PDB coordinates weekly updates of
the PDB archive with other wwPDB Data
Centers in Europe and Asia.
​​
PDB
archival format and data standards
are defined by the PDBx/mmCIF dictionary(mmCIF.wwpdb.org). At present, PDBx/
mmCIF is jointly maintained by RCSBPDB, our wwPDB partners, and the
wwPDB PDBx/mmCIF Working Group.

PDB ARCHIVE BY

EXPERIMENTALTECHNIQUE

X-ray
Diffraction 85%
3D Electron
Microscopy 8%
NMR Spectroscopy 7%

PDB ARCHIVE

214,121

Released atomic
coordinate entries

PDB ARCHIVE BY

MOLECULE TYPE

Proteins, Peptides,
and Viruses 87%
Protein/Nucleic Acid
Complexes 6%
Protein/Oligosaccharide 5%
Nucleic Acids 2%2023 ANNUAL REPORT | PAGE 5

DATA EXPLORATIONSERVICE 32023 HIGHLIGHTS

Supporting PDB Data Consumers in the US and aroundthe world through our open-access web portal RCSB.org
that provides tools for structure visualization,
analysis, and download.
RCSB.org is one of the most heavily usedbiological data resources worldwide. For
2023, internal analytics reported ~8.2
million unique IP addresses, making~3.5 billion requests, downloads, andviews. During the same period, Google
Analytics estimated that RCSB.org hosted~5.2 million unique users (~20% fromUSA) viewing ~63 million web pages.
The website supports a broad rangeof skill levels and interests. In addition
to retrieving 3D structure data, RCSB.org
users access comparative data, andexternal annotations from resources
such as Comprehensive Antibiotic
Resistance Database (CARD) and Pharos,
a comprehensive knowledge base for
RCSB PDB APIs
RCSB PDB services are accessed via
our website (RCSB.org) and public
API endpoints for programmaticaccess, with two main APIs: Data
(data.rcsb.org) and Search(search.rcsb.org).
Supporting API services include
the 1D Coordinate Server API(1d-coordinates.rcsb.org) that servesalignments between structural andsequence databases and integrates
protein positional features frommultiple resources and Alignment API(alignment.rcsb.org) that serves
as a comprehensive platform forthe seamless computation of
structure alignments.

RCSB PDB services go well beyond theoriginal structure and scientific publication.
Each PDB structure is represented by a
Structure Summary page that organizes
access to important information, including
a snapshot of the validation report andother high-level content, annotations,sequence information, sequence similarity
clusters, and experimental data. These
data are updated weekly, which meansthat while the corresponding scientificpublication remains static, RCSB PDB
delivers contemporary views ofexperimentally-determined PDB
structures and CSMs.
The research-focused RCSB.org web
portal offers a rich collection of softwaretools and features that can be used tosearch, browse, analyze, and visualize
PDB data. These include powerful searchservices as well as interactive analyticaland visualization tools such as the Mol*
molecular graphics system, sequenceannotations view, and specialized tools

clients (unique IP addresses)~63 million

web page views~3.5 billion

requests/interactions(downloads, service usage,
web page content views)
that provide redundancy-reduced “groups”
view of similar data. The Pairwise
Structure Alignment Tool can align one
or more protein chains to a reference
structure in a pairwise manner, forsimultaneous analysis and visualizationof 3D structure alignments and structurebased 1D sequence alignments.
3D structure similarity and motif searches
can be executed based on 3D atomic
coordinates uploaded by the user. This
allows identification of similarities between
uploaded coordinates to experimentallydetermined PDB structures and CSMs
available from RCSB.org.
RCSB.org will continue to expand its
one-stop shop for studying the 3D
structures of biomolecules by providing
PDB data consumers with access to CMSs
of model organisms, select pathogens,agriculturally-important plants, andorganisms crucial in the battle against
climate change.

DATA

1D
COORDINATESERVERAPI

the Druggable Genome. Gene Ontology,
InterPro, and Pharos annotations werealso made available for the computed
structure models (CSMs) in addition toexperimentally-determined PDB structures.

~8.2 million

SEARCHAPI

API
ALIGNMENTAPI

2023 ANNUAL REPORT | PAGE 6

Pairwise alignment tool on RCSB.org showing structural comparison of
PDB structures of toxins produced by sea anemones

TRAINING, OUTREACH, AND EDUCATION
Building and supporting the broad PDB user community
with a wide range of resources for understanding
3D biostructures.
PDB-101 (PDB101.RCSB.org) is an online
portal for exploring the world of proteinsand nucleic acids. The diverse shapes andfunctions of biological macromolecules
help explain aspects of fundamental
biology, biomedicine, and bioenergy,
from protein synthesis to health anddisease to biofuels.

biology, biomedicine, bioengineering/biotechnology, and energy sciences in
3D by a diverse and multidisciplinary
user community.

In 2023, ~548,000 users visited
PDB-101, viewing >1.8 million pages.

Other PDB-101 content released this year
included a 2024 calendar highlighting theStructural Biology of Peak Performance;
new features Exploring the Structural
Biology of Bioenergy; Exploring theStructural Biology of Viruses; andExploring the Structural Biology of Healthand Nutrition; an introduction to APIs; andTraining materials, such as the Guide toUnderstanding PDB Data and webinars,
are available to help graduate students,
postdoctoral scholars, and researchers
use PDB data and RCSB PDB tools.

Education Materials, such as Curriculum
Modules, provide lessons and activities forteaching and learning.

SERVICE 42023 HIGHLIGHTS~548,000

unique users>1.8 million

web page views>850,000

video views including molecularanimations, training materials,
and tutorials
Global Health articles highlighting diabetes
drugs used for blood glucose management,
weight loss, and other topics.
PDB-101 molecular animation videos,
webinar recordings, and tutorials
are hosted on YouTube. The channel(RCSBProteinDataBank) has ~85,000
subscribers; videos were viewed
858,703 times in 2023.

Popular training courses in 2023
included Leveraging RCSB PDB APIs for
Bioinformatics Analyses and Machine
Learning; Use PDB Data To Their Full
Extent: Understanding PDBx/mmCIF;
and Python Scripting for Biochemistry &Molecular Biology II.
Outreach content, including the Moleculeof the Month series and molecularanimations, demonstrate how PDB data
can be used to understand fundamental
Illustrations from “Exploring the Structural Biology of Health and Nutrition” and “Exploring
the Structural Biology of Viruses”.

SCIENTIFIC SUPPORT AND USER ENGAGEMENTRCSB PDB regularly participates in meetings and scientific societies, hosts
Working Groups, and convenes method-specific Task Forces. Recognized experts
in fields, including but not limited to, structural biology, cell and molecular biology,
computational biology, information technology, and education serve as advisors
to the RCSB PDB.

All training resources are accessible
through the PDB-101 website from the
new “Train” section in the top menu.

Depositors and PDB Data Consumers are supported by responsive Help Desks
covering all RCSB PDB and wwPDB services. User feedback helps inform
prioritization and resource development to meet the needs of diverse
research and education communities.
2023 ANNUAL REPORT | PAGE 7

RCSB.ORG • INFO@RCSB.ORG
RCSB PDB is managed by the members of the
Research Collaboratory for Structural Bioinformatics:
Rutgers, UCSD/SDSC, and UCSF

FUNDINGRCSB PDB core operations are funded by National Science Foundation(DBI-1832184), the US Department of Energy (DE-SC0019749),
and the National Cancer Institute, National Instituteof Allergy and Infectious Diseases, and National
Institute of General Medical Sciences of
the National Institutes of Health under
grant R01GM133198.

CITE RCSB PDB
The Protein Data Bank (2000) Nucleic Acids Research 28: 235-242.
doi: 10.1093/nar/28.1.235

ABOUT THE COVER
Acknowledgement: Illustration by David S. Goodsell,
RCSB Protein Data Bank and Scripps Research.
doi: 10.2210/rcsb_pdb/goodsell-gallery-048
Snapshots from the life cycle of bacteriophage T4.
At left, a bacteriophage (red) is injecting its DNA genome (white)
into an Escherichia coli cell. At center, the bacteriophage has takenover the cell, destroying the cellular DNA (purple) and forcing
the cell to make many new copies of bacterial virus. At right, thebacteriophage produces a channel-forming protein that pierces theinner cell membrane, allowing lysozyme enzymes to break down
the peptidoglycan sheath that supports the cell. The cell bursts,
releasing several hundreds of new bacteriophages.

RCSB Protein Data Bank (RCSB.org): Delivery of experimentallydetermined PDB structures alongside one million computed
structure models of proteins from artificial intelligence/machinelearning (2023) Nucleic Acids Research 51: D488–D508
doi: 10.1093/nar/gkac1077
RCSB Protein Data Bank: Tools for visualizing and understanding
biological macromolecules in 3D (2022) Protein Science 31: e4482
doi: 10.1002/pro.4482
RCSB Protein Data Bank: Efficient Searching and Simultaneous
Access to One Million Computed Structure Models Alongside the PDB
Structures Enabled by Architectural Advances (2023)
Journal of Molecular Biology 435: 167994
doi: 10.1016/j.jmb.2023.167994
RCSB PDB is a member of the wwPDB
organization | wwPDB.org

Many structures of parts of bacteriophage T4 are available in the
PDB archive, including the head that holds the DNA in PDB ID 7vs5
(mature form) and 7vrt (immature form), and the baseplate with
the injection machinery in PDB ID 5iv5.

PDB is a CoreTrustSeal Board certified
Trusted Digital Repository.

PDB is a Global Core Biodata Resource
whose long term funding and sustainability
is of fundamental importance to biologicaland life science communities.

FOLLOW US/RCSBPDB/RCSBProteinDataBank/buildmodels/rcsb