The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

Supplementary data are available at Bioinformatics online.

SUMMARY OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the Protein Data Bank (PDB) archive, has been developed as a global collaboration by the Worldwide Protein Data Bank (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

SUMMARYSialic acid Ig-like binding lectins are important mediators of recognition and signaling events among myeloid cells. To investigate the molecular mechanism underlying Siglec functions, we have determined the crystal structure of the two N-terminal extracellular domains of a human myeloid cell inhibitory receptor Siglec-5 (CD170) and its complexes with two sialylated carbohydrates. The native structure revealed an unusual conformation of the CC′ ligand specificity loop and a unique interdomain disulfide bond. The α(2,3)-sialyllactose and α(2,6)-sialyllactose complexed structures showed a conserved sialic acid recognition motif that involves both Arg 124 and a portion of the Gstrand in the V-set domain forming β-sheet-like hydrogen bonds with the glycerol side chain of the sialic acid. Only few direct protein contacts to the sub-terminal sugars are observed and mediated by the highly variable GG′ linker and CC′ loop. These structural observations in conjunction with surface plasmon resonance binding assays provide mechanistic insights into the linkage-dependent Siglec carbohydrate recognition and suggest that Siglec-5 and other CD33-related Siglec receptors are more promiscuous in sialo-glycan recognition than previously understood.

Natural killer (NK) cells are a group of innate immune cells that carry out continuous surveillance for the presence of virally infected or cancerous cells. The natural cytotoxicity receptor (NCR) NKp30 is critical for the elimination of a large group of tumor cell types. Although several ligands have been proposed for NKp30, the lack of a conserved structural feature among these ligands and their uncertain physiological relevance has contributed to confusion in the field and hampered a full understanding of the receptor. To gain insights into NKp30 ligand recognition, we have determined the crystal structure of the extracellular domain of human NKp30. The structure displays an I-type Ig-like fold structurally distinct from the other natural cytotoxicity receptors NKp44 and NKp46. Using cytolytic killing assays against a range of tumor cell lines and subsequent peptide epitope mapping of a NKp30 blocking antibody, we have identified a critical ligand binding region on NKp30 involving its F strand. Using different solution binding studies, we show that the N-terminal domain of B7-H6 is sufficient for NKp30 recognition. Mutations on NKp30 further confirm that residues in the vicinity of the F strand, including part of the C strand and the CD loop, affect binding to B7-H6. The structural comparison of NKp30 with CD28 family receptor and ligand complexes also supports the identified ligand binding site. This study provides insights into NKp30 ligand recognition and a framework for a potential family of unidentified ligands.

Liquid Ga was used as a solvent to explore the phase formation between rare-earth metals (REs), Ni, and a tetrelide (Tt = Si, Ge). The reactions were performed in excess liquid Ga at 850 °C. Two new phases of general formulas RE0.67Ni2Ga5 - x Tt x and RE0.67Ni2Ga6 - x Tt x were found and structurally characterized. The Co analogues of the latter RE0.67Co2Ga6 - x Ge x (RE = Y, Gd) were also prepared. Single-crystal X-ray data:  The first group of compounds RE0.67Ni2Ga5 - x Tt x crystallizes in the hexagonal space group P63/mmc with a structure related to the RE2 - x Pt4Ga8+ y type (Sm0.53Ni2Ga5 - x Ge x , a = 4.1748(7) Å, c = 16.007(4) Å, V = 241.61(8) Å3, Z = 2; Y0.59Ni2Ga5 - x Ge x , a = 4.1344(11) Å, c = 15.887(6) Å, V = 235.18(12) Å3, Z = 2; Tb0.67Ni2Ga5 - x Si x , a = 4.1415(11) Å, c = 15.843(6) Å, V = 235.33(12) Å3, Z = 2; Ho0.67Ni2Ga5 - x Ge x , a = 4.1491(4) Å, c = 15.877(2) Å, V = 236.71(5) Å3, Z = 2). The second group RE0.67Ni2Ga6 - x Tt x crystallizes in P6̄m2 (Gd0.67Ni2Ga6 - x Ge x , a = 4.1856(10) Å, c = 9.167(3) Å, V = 139.08(7) Å3, Z = 1; Sm0.67Ni2Ga6 - x Si x , a = 4.1976(8) Å, c = 9.159(3) Å, V = 139.76(5) Å3, Z = 1) in a structure related to the ErNi3Al9 structure type with disorder in the RE−Ga plane. Dy0.67Ni2Ga6 - x Ge x crystallizes in space group P3̄1c (a = 7.2536(8) Å, c = 18.308(3) Å, V = 834.21(2) Å3, Z = 6) with partial disorder in the RE−Ga plane. The structures of these two groups of compounds are related to each other and contain similar building motifs, namely Ga n [NiGa2 - x /2Ge x /2]2 slabs and RE0.67Ga monatomic layers which alternate along the c-direction, forming a 3D structure. The parameter x and the position of the tetrelide in the structure were determined by single-crystal neutron diffraction. Complete or partial disorder of the RE and Ga atoms is observed in the RE−Ga plane. The origin of the disorder lies in the extensive and random stacking faults of ordered RE−Ga planes, which apparently slide easily in the ab plane and create an averaged disordered picture. Electrical conductivity and thermopower measurements indicate that these compounds are metallic conductors. The magnetic measurements show antiferromagnetic ordering at ∼3−4 K and Curie−Weiss behavior at higher temperatures with the values of μeff close to those of RE3+ free ions. Strong 2-fold crystal field anisotropy is observed for the heavy RE analogues. The anisotropy constants K 2 para calculated from the Weiss constant anisotropy for heavy RE analogues are reported.