Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Database URL: https://www.wwpdb.org/.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (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.

Small molecule annotation for the Protein Data Bank.

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called "group" was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently.

Crystal structure of human natural cytotoxicity receptor NKp30 and identification of its ligand binding site.

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.

Polygallide RE2MGa9Ge2 (RE = Ce, Sm; M = Ni, Co) phases grown in molten gallium.

The quaternary intermetallics Ce2CoGa9Ge2, Ce2NiGa9Ge2, and Sm2NiGa9Ge2 were prepared by reacting elemental metals in excess of gallium at 850 degrees C. The title compounds crystallize in the tetragonal space group P4/nmm in the Sm2Ni(Si(1-x)Ni(x))Al4Si6 structure type with cell parameters a = 5.9582(5) A, c = 15.0137(18) A, and a = 5.9082(17) A, c = 14.919(6) A, Z = 2, for Ce2CoGa9Ge2 and Sm2NiGa9Ge2, respectively. The structures are composed of covalently bonded three-dimensional networks of [CoGa9Ge2] in which the rare-earth metals fill the voids forming a 2D square net. The structures of RE2MGa9Ge2 are Ga-rich and possess extensive Ga-Ga bonding even though the Ga atoms do not form a network on their own. Magnetic susceptibility measurements for Ce2CoGa9Ge2 and Ce2NiGa9Ge2 show Curie-Weiss paramagnetism, consistent with presence of Ce(3+) ions. Magnetocrystalline anisotropy was observed for Ce2NiGa9Ge2, with the magnetically easy axis lying along the [001] crystallographic direction. A transition to an antiferromagnetic state was observed below 4 K in the easy direction of magnetization. In the magnetically hard direction of the basal plane, paramagnetic behavior was observed down to 1.8 K.

Structural implications of Siglec-5-mediated sialoglycan recognition.

Sialic acid (Sia) Ig-like binding lectins are important mediators of recognition and signaling events among myeloid cells. To investigate the molecular mechanism underlying sialic acid Ig-like lectin (Siglec) functions, we determined the crystal structure of the two N-terminal extracellular domains of 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 alpha(2,3)- and alpha(2,6)-sialyllactose complexed structures showed a conserved Sia recognition motif that involves both Arg124 and a portion of the G-strand in the V-set domain forming beta-sheet-like hydrogen bonds with the glycerol side chain of the Sia. Only few protein contacts to the subterminal 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 linkage-dependent Siglec carbohydrate recognition and suggest that Siglec-5 and other CD33-related Siglec receptors are more promiscuous in sialoglycan recognition than previously understood.

Tb4FeGe8 grown in liquid gallium: trans-cis chains from the distortion of a planar Ge square net.

The ternary germanide Tb4FeGe8 was obtained from Ga flux reactions. The crystal structure studied with single-crystal X-ray diffraction revealed the existence of an orthorhombic average substructure (Cmcm, Z=1) with cell parameters a = 4.1118(14) A, b=15.844(5) A, and c=3.9885(15) A. The refinement [I > 2sigma(I)] converged to final residuals R1/wR2 = 0.0363/0.0893. The average structure (CeNiSi2-type) consists of a 3D [Fe1/4Ge2] framework where Ge atoms form a square net and Fe atoms reside alternatively above and below it with only 1/4 occupation probability. X-ray and electron diffraction studies showed a modulation in the Ge net. The modulated structure was refined based on a 4-fold monoclinic supercell (P2(1)/n) with parameters a = 5.7315(11) A, b = 15.842(3) A, c = 11.438(2) A, and beta = 91.724(4) degrees with R1/wR2 = 0.0643/0.1735 and uncovered a severe distortion of the Ge square net. The Ge atoms are displaced to form an array of cis-trans chains. The Ge-Ge distances within these chains are distinctively bonding, whereas those between the chains are nonbonding. Results of the electronic structure calculations and magnetic measurements are also reported. The structural distortions found in Tb4FeGe8 cast a doubt onto the correctness of many of the reported REM1-xGe2 disordered compounds and call for reinvestigation.

Intermetallics as zintl phases: Yb2Ga4Ge6 and RE3Ga4Ge6 (RE=Yb, Eu): structural response of a [Ga4Ge6]4- framework to reduction by two electrons.

Two new intermetallic compounds, Yb(2)Ga(4)Ge(6) and Yb(3)Ga(4)Ge(6), were obtained from reactions in molten Ga. A third compound, Eu(3)Ga(4)Ge(6), was produced by direct combination of the elements. The crystal structures of these compounds were studied by single-crystal X-ray diffraction. Yb(2)Ga(4)Ge(6) crystallizes in an orthorhombic cell with a=4.1698(7), b=23.254(4), c=10.7299(18) A in the polar space group Cmc2(1). The structure of RE(3)Ga(4)Ge(6) is monoclinic, space group C2/m, with cell parameters a=23.941(6), b=4.1928(11), c=10.918(3) A, beta=91.426(4) degrees for RE=Yb, and a=24.136(2), b=4.3118(4), c=11.017(1) A, beta=91.683(2) degrees for RE=Eu. The refinement [I>2 sigma(I)] converged to the final residuals R(1)/wR(2)=0.0229/0.0589, 0.0411/0.1114, and 0.0342/0.0786 for Yb(2)Ga(4)Ge(6), Yb(3)Ga(4)Ge(6), and Eu(3)Ga(4)Ge(6), respectively. The structures of these two families of compounds can be described by a Zintl concept of bonding, in which the three-dimensional [Ga(4)Ge(6)](n-) framework serves as a host and electron sink for the electropositive RE atoms. The structural relation of RE(3)Ga(4)Ge(6) to of Yb(2)Ga(4)Ge(6) lies in a monoclinic distortion of the orthorhombic cell of Yb(2)Ga(4)Ge(6) and reduction of the [Ga(4)Ge(6)] network by two electrons per formula unit. The results of theoretical calculations of the electronic structure, electrical transport data, and thermochemical and magnetic measurements are also reported.

REMGa3Ge and RE3Ni3Ga8Ge3 (M = Ni, Co; RE = rare-earth element): new intermetallics synthesized in liquid gallium. X-ray, electron, and neutron structure determination and magnetism.

New quaternary intermetallic phases REMGa(3)Ge (1) (RE = Y, Sm, Tb, Gd, Er, Tm; M = Ni, Co) and RE(3)Ni(3)Ga(8)Ge(3) (2) (RE = Sm, Gd) were obtained from exploratory reactions involving rare-earth elements (RE), transition metal (M), Ge, and excess liquid Ga the reactive solvent. The crystal structures were solved with single-crystal X-ray and electron diffraction. The crystals of 1 and 2 are tetragonal. Single-crystal X-ray data: YNiGa(3)Ge, a = 4.1748(10) A, c = 23.710(8) A, V = 413.24(2) A(3), I4/mmm, Z = 4; Gd(3)Ni(3)Ga(8)Ge(3), a = 4.1809(18) A, c = 17.035(11) A, V = 297.8(3) A(3), P4/mmm, Z = 1. Both compounds feature square nets of Ga atoms. The distribution of Ga and Ge atoms in the REMGa(3)Ge was determined with neutron diffraction. The neutron experiments revealed that in 1 the Ge atoms are specifically located at the 4e crystallographic site, while Ga atoms are at 4d and 8g. The crystal structures of these compounds are related and could be derived from the consecutive stacking of disordered [MGa](2) puckered layers, monatomic RE-Ge planes and [MGa(4)Ge(2)] slabs. Complex superstructures with modulations occurring in the ab-plane and believed to be associated with the square nets of Ga atoms were found by electron diffraction. The magnetic measurements show antiferromagnetic ordering of the moments located on the RE atoms at low temperature, and Curie-Weiss behavior at higher temperatures with the values of mu(eff) close to those expected for RE(3+) free ions.

Isolation of the new cubic phases RE4FeGa(12-x)Ge(x) (RE = Sm, Tb; x = 2.5) from molten gallium: single-crystal neutron diffraction study of the Ga/Ge distribution.

The compounds RE4FeGa(12-x)Ge(x) (RE = Sm, Tb) were discovered in reactions employing molten Ga as a solvent at 850 degrees C. However, the isostructural Y4FeGa(12-x)Ge(x) was prepared from a direct combination reaction. The crystal structure is cubic with space group Imm, Z = 2, and a = 8.657(4) A and 8.5620(9) A for the Sm and Tb analogues, respectively. Structure refinement based on full-matrix least squares on F(o)2 resulted in R1 = 1.47% and wR2 = 4.13% [I > 2(I)] for RE = Sm and R1 = 2.29% and wR2 = 7.12% [I > 2(I)] for RE = Tb. The compounds crystallize in the U4Re7Si6 structure type, where the RE atoms are located on 8c (1/4, 1/4, 1/4) sites and the Fe atoms on 2a (0, 0, 0) sites. The distribution of Ga and Ge in the structure, investigated with single-crystal neutron diffraction on the Tb analogue, revealed that these atoms are disordered over the 12d (1/4, 0, 1/2) and 12e (x, 0, 0) sites. The amount of Ga/Ge occupying the 12d and 12e sites refined to 89(4)/11 and 70(4)/30%, respectively. Transport property measurements indicate that these compounds are metallic conductors. Magnetic susceptibility measurements and Mössbauer spectroscopy performed on the Tb analogue show a nonmagnetic state for Fe, while the Tb atoms carry a magnetic moment corresponding to a mu(eff) of 9.25 mu(B).