wwPDB 2019 News

Contents

06/11/2019 Improvements to visualization of ligand validation and electron density maps in the wwPDB validation report
06/03/2019 A tribute to Prof. Michael G. Rossmann
04/16/2019 Announcement of mandatory mmCIF submission published in Acta Cryst D
04/09/2019 Job Posting: Founding Director, Protein Data Bank China
03/19/2019 The PDB Archive Reaches a Significant Milestone
02/19/2019 Mandatory PDBx/mmCIF format files submission for MX depositions
02/13/2019 Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures, Paper Retractions
01/02/2019 Time-stamped Copies of the PDB Archive Available

06/11/2019

Improvements to visualization of ligand validation and electron density maps in the wwPDB validation report

Our recent update to the wwPDB validation reports provides much clearer validation information for ligands.

We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by crystallography, 3-dimensional views of electron density.

We also provide calculated electron density map coefficients which were used to generate the analysis in the validation reports.

Ligand Validation

We have collaborated with Global Phasing Ltd to integrate the ligand visualization from buster-report into the wwPDB validation report, as recommended by the wwPDB/CCDC/D3R Ligand Validation Workshop. The ligand visualization will be available for ligands that have been designated as "Ligand of Interest" by the depositor and ligands with a molecular weight greater than 250 Daltons that have outliers.

The following ligand instance of NAP was chosen intentionally as a representative of sub-optimal quality in both the ligand model and its agreement with the X-ray data.

Geometric analysis provided by CCDC Mogul will be highlighted on a 2D diagram of the ligand, as shown below.

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In addition to geometric validation for ligands, for X-ray diffraction PDB entries the wwPDB validation report also presents images displaying the ligand and the surrounding electron density map.

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Electron Density Map Coefficient Files

We are now providing depositors with electron density map coefficient files (2mFo-DFc and mFo-DFc) from the wwPDB validation pipeline alongside the wwPDB validation report. The electron density map coefficients generated for wwPDB validation reports will be made available to end users in the PDB archive as new entries are released and for existing entries when validation reports for the PDB archive are recalculated.

We hope that these changes to the wwPDB validation pipeline will help depositors to interpret the validation information provided for PDB entries more easily. If you have any queries, please contact the wwPDB at deposit-help@mail.wwpdb.org.

06/03/2019

A tribute to Prof. Michael G. Rossmann

All of us at wwPDB were deeply saddened to hear of the recent passing of Prof. Michael G. Rossmann and our condolences go out to his family and friends at this time. Michael contributed so much to the field of structural biology and was a great supporter of the wwPDB and our activities. Here we would like to share our own tribute to Michael and his contribution to the PDB archiving efforts.

Michael has had an esteemed structural biology career, with over 300 structures to his name in the PDB, spanning from 1977 through to 2019. He also helped to develop the molecular replacement technique, enabling phasing of data in X-ray crystallography, which has been used for structure determination of around 100,000 PDB entries to date. One of Michael's key discoveries is of the Rossmann fold, a structural motif commonly found in enzymes that bind to dinucleotide cofactors. It's importance is highlighted by the fact that around 20,000 structures in the PDB contain a Rossmann fold motif, another lasting legacy of his work within the PDB archive.

Michael also made huge contributions to the field of virology, with hundreds of his virus structures archived in the PDB. This includes the first structure determined of the human rhinovirus, otherwise known as the common cold. His work has significantly improved the knowledge of virus structure and function, supporting development of new therapeutics to treat and prevent viral infections.

Michael was a member of the wwPDB advisory committee for four years, serving on the board from 2009 to 2012, and was also involved in advisory committees for RCSB PDB and EMDataBank. During this time, he provided much advice and guidance to the wwPDB, helping to shape the archiving activities during this time and into the future. Helen Berman, former director of the RCSB Protein Data Bank, highlights how Michael "was an active supporter of the Protein Data Bank from its inception in the early 1970s", while Haruki Nakamura, former head of Protein Data Bank Japan (PDBj), speaks of "always being impressed by his thoughtful comments about the activities of the wwPDB." Haruki adds: "Michael understood the importance of archiving raw experimental data and he had promoted 'data science' for many years."

Gerard Kleywegt, former head of Protein Data Bank in Europe (PDBe), pays tribute to Michael as a person, describing him as "a dynamo, with an enormous zest for life and science who got along with almost everybody." Gerard also emphasises how, even in recent months, "he was still collecting data himself" and recalls Michael's dismay at a grant funding rejection and how "he simply could not understand how that was possible as it was obviously solid science."

We are indebted to Michael for his help and support to the wwPDB and to the structural biology community as a whole. As Helen Berman puts it: "Michael was truly unique in his contributions to structural biology and we will be forever grateful for all he did."

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04/16/2019

Announcement of mandatory mmCIF submission published in Acta Cryst D

A new publication in Acta Cryst D announces the mandatory submission of PDBx/mmCIF to the PDB for crystallographic depositions. The authorship includes representatives from the major crystallographic structure refinement software packages, in addition to all wwPDB partners.

We are pleased to share our publication “Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)”, published in Acta Cryst D. This publication emphasises that PDBx/mmCIF will be the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), including X-ray, neutron, fiber, and electron diffraction methods via OneDep starting July 1st 2019.

Refmac (CCP4), Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. Inclusion of representatives from each these softwares within the authorship of the publication highlights the commitment of the crystallographic software community to the PDBx/mmCIF data model. The deposition of PDBx/mmCIF format files will improve the efficiency of the deposition process and enhance validation through capture of the more extensive experimental metadata supported by PDBx/mmCIF, compared to the legacy PDB format.

More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website.

04/09/2019

Job Posting: Founding Director, Protein Data Bank China

A job is opening for a founding director of Protein Data Bank China (PDBc), with the primary task of establishing structure archiving activities in China. The position will be a joint between the NCPSS, iHuman and SIAIS at ShanghaiTech University, with the successful candidate working with the Worldwide Protein Data Bank (wwPDB) Core Members (RCSB PDB and BMRB in the US, PDBe in Europe, and PDBj in Japan) to satisfy the requirements for PDBc to become a member of the wwPDB organization.

Details are available from ShanghaiTech University

03/19/2019

The PDB Archive Reaches a Significant Milestone

With this week's update, the PDB archive has passed the milestone of 150,000 entries, and now contains a total of 150,145.

Established in 1971, this central, public archive has reached this milestone thanks to the efforts of structural biologists throughout the world who collectively contribute a wealth of experimentally-determined protein and nucleic acid structure data, which is made available to researchers all around the world, across many different disciplines.

Four wwPDB data centers support online access to three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy. The archive is large, containing more than 1.9 million files related to these PDB entries and requiring more than 512 gigabytes of storage.

The archive reached the landmark of 100,000 entries in 2014, the International Year of Crystallography. Since that record was set, the PDB continued to grow rapidly, both in number of deposited structures and in the complexity of the data. This growth has been supported by the launch of OneDep, a common global system for deposition, validation, and biocuration of PDB data for supported experimental methods. The OneDep system and the underlying PDBx/mmCIF archive format enable the PDB archive to adapt over time to meet the challenges posed by developments in structural biology. More than 41,000 structures that have been deposited, annotated, and validated using OneDep have now been released into the PDB archive, with many more entries updated to ensure consistency of the archive.

With this week's regular update, the PDB welcomes 262 new structures into the archive. These structures join others vital to research and education in fundamental biology, biomedicine, and bioenergy. Since its inception, the size of the archive has increased tenfold roughly every 10-15 years: the PDB reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000. Now that the 150,000th is made available, more than half of the archive has been released in the past ten years.

The scientific community eagerly awaits the next 150,000 structures and the invaluable knowledge these new data will bring. However, the increasing number, size and complexity of biological data being deposited in the PDB and the emergence of hybrid structure determination methods constitute major challenges for the management and representation of structural data. wwPDB will continue to work with the community to meet these challenges and ensure that the archive maintains the highest possible standards of quality, integrity, and consistency.

Development and future of the PDB archive and wwPDB organization is described in the new reference publication for the PDB archive: Protein Data Bank: the single global archive for 3D macromolecular structure data (Nucleic Acids Res., 2019) and many other papers, including Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (Methods in Molecular Biology, 2017), How community has shaped the Protein Data Bank (Structure, 2013), and Creating a Community Resource for Protein Science (Protein Science, 2012). A full list is available.

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02/19/2019

Mandatory PDBx/mmCIF format files submission for MX depositions

Submission of PDBx/mmCIF format files for crystallographic depositions to the PDB will be mandatory from July 1st 2019 onward. PDB format files will no longer be accepted for deposition of structures solved by MX techniques.

PDBx/mmCIF will be the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), including X-ray, neutron, fiber, and electron diffraction methods via OneDep starting July 1st 2019. The deposition of PDBx/mmCIF format files will improve the efficiency of the deposition process and enhance validation through capture of the more extensive experimental metadata supported by PDBx/mmCIF, compared to the legacy PDB format. PDB entries with 100,000 or more atoms, and those with multiple character chain IDs are already not supported by the legacy PDB format. In addition, by 2021, we anticipate the PDB Chemical Component Identifier will need to be extended beyond three characters, which will necessarily result in full retirement of files in the PDB Core Archive that utilize the legacy PDB format.

Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract and MAXIT. More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website.

The PDBx/mmCIF Working Group has committed to the PDBx/mmCIF data model. PDBx/mmCIF is also supported by visualization software applications, including Jmol/JSMol, LiteMol, Chimera, OpenRasMol, CCP4MG, COOT, PyMOL, VMD, MolMil, and NGL. In addition, other data resources, such as the Protein Model Portal and SASBDB, have adopted and extended the PDBx/mmCIF framework for data representation.

If you have any queries or comments regarding these changes, please contact the wwPDB consortium via deposit-help@mail.wwpdb.org.

02/13/2019

Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures, Paper Retractions

In 2018, The Office of Research Integrity (ORI) of the U.S. Department of Health and Human Services announced their final Research Misconduct Finding in the case of H.M. Krishna Murthy. It was found that Murthy reported falsified and/or fabricated research in 10 journal publications and 12 corresponding PDB structures. While the ORI was gathering and evaluating evidence in this case, 5 Murthy structures in the PDB were obsoleted in accord with wwPDB policies, in response to retraction of 4 journal publications. Following a formal request from ORI, received on April 23rd 2018, the remaining 7 Murthy structures in the PDB were obsoleted, again in accord with wwPDB policies. ORI conduct within its investigations is designed to ensure due process for individuals accused of research misconduct, and strict confidentiality is maintained throughout. Only (the final?) findings of research misconduct are made public.

In December 2009, the University of Alabama at Birmingham (UAB) announced that it planned to retract 12 PDB entries and 10 related publications authored by H.M. Krishna Murthy, in his capacity as Principal Investigator and UAB employee. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, 5 of the structures were obsoleted upon retraction of the related publications by the journals. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, the remaining 7 structures were obsoleted upon receipt of the ORI request.

Since that time, the 5 publications associated with the 7 structures have been retracted by the journals. A detailed PDB history of this case is available.

  • RETRACTED: Crystal structure of a complement control protein that regulates both pathways of complement activation and binds heparan sulfate proteoglycans (2001) Cell 104, 301-311 doi: 10.1016/S0092-8674(01)00214-8
  • Retraction of "Structures of Apolipoprotein A-II and a Lipid-Surrogate Complex Provide Insights into Apolipoprotein-Lipid Interactions" (2018) Biochemistry 57, 6044 doi: 10.1021/acs.biochem.8b00956
  • Retraction for Ganesh et al., Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation (2018) Proc Natl Acad Sci USA 115, E6965 doi: 10.1073/pnas.1806429115
  • Retraction of "Structural Basis for Antagonism by Suramin of Heparin Binding to Vaccinia Complement Protein" (2018) Biochemistry 57, 6043 doi: 10.1021/acs.biochem.8b00955
  • Retraction for Ajees et al., Crystal structure of human apolipoprotein A-I: Insights into its protective effect against cardiovascular diseases (2018) Proc Natl Acad Sci USA 115, E6966 doi: 10.1073/pnas.1806430115

Structure Validation and the Role of the PDB as an Archival Data Resource

The PDB is an archival resource that stores, annotates, and disseminates structure models and their related experimental data. The wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008), NMR (in 2009), and (in collaboration with the EMDataBank) Cryo-EM (in 2010) to advise on the most suitable criteria to use for validating structure entries (model, experimental data, and fit of model to data) when they are deposited. Recommendations of these validation task forces have been implemented as part of the wwPDB OneDep system for deposition, annotation, and validation of PDB structures.

The results of these wwPDB validation procedures are captured in a report that is provided to depositors and can be transmitted by them to the journal to which the corresponding manuscript is submitted. Availability of such a report greatly facilitates assessment of the reliability of structural data and its interpretation by journal editors and referees alike. The wwPDB has urged journals publishing structural data on biological macromolecules to require submission of the wwPDB validation report together with the manuscript. The continuing mission of the wwPDB partners is to safeguard the integrity and improve the quality of the structural archive, with the support of the international structural biology community.

For additional information, see

01/02/2019

Time-stamped Copies of the PDB Archive Available

A snapshot of the PDB archive (ftp://ftp.wwpdb.org) as of January 1, 2019 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20190101 includes the 147,610 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot is 1,529 GB.