skip to main content

Title: CCDC 2181759: Experimental Crystal Structure Determination
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset forMore>>
; ;
Cambridge Crystallographic Data Centre
Publication Year:
Crystal Structure Experimental 3D Coordinates Crystal System Space Group Cell Parameters Crystallography
Award ID(s):
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract
    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
    Related Article: Jonathan D. Dabbs, Diane A. Dickie, W. Dean Harman|2022|CSD Communication|||
  2. We present a prototype database for quasi two-dimensional crystalline organic conductors and superconductors based on molecules related to bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF, ET). The database includes crystal structures, calculated electronic structures, and experimentally measured properties such as the superconducting transition temperature and critical magnetic fields. We obtained crystal structures from the Cambridge Structural Database and created a crystal structure analysis algorithm to identify cation molecules and execute tight binding electronic structure calculations. We used manual data entry to encode experimentally measured properties reported in publications. Crystalline organic conductors and superconductors exhibit a wide variety of electronic ground states, particularly those with correlations. We hope that this database will ultimately lead to a better understanding of the fundamental mechanisms of such states.
  3. Abstract

    Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic andmore »diseases caused by other coronaviruses.

    « less
  4. Tuning the properties of atomic crystals in the two-dimensional (2D) limit is synthetically challenging, but critical to unlock their potential in fundamental research and nanotechnology alike. 2D crystals assembled using superatomic blocks could provide a route to encrypt desirable functionality, yet strategies to link the inorganic blocks together in predetermined dimensionality or symmetry are scarce. Here, we describe the synthesis of anisotropic van der Waals crystalline frameworks using the designer superatomic nanocluster Co 3 (py) 3 Co 6 Se 8 L 6 (py = pyridine, L = Ph 2 PN(Tol)), and ditopic linkers. Post-synthetically, the 3D crystals can be mechanically exfoliated into ultrathin flakes (8 to 60 nm), or intercalated with the redox-active guest tetracyanoethylene in a single-crystal-to-single-crystal transformation. Extensive characterization, including by single crystal X-ray diffraction, reveals how intrinsic features of the nanocluster, such as its structure, chirality, redox-activity and magnetic profile, predetermine key properties of the emerging 2D structures. Within the nanosheets, the strict and unusual stereoselectivity of the nanocluster's Co edges for the low symmetry (α,α,β) isomer gives rise to in-plane structural anisotropy, while the helically chiral nanoclusters self-organize into alternating Δ- and Λ-homochiral rows. The nanocluster's high-spin Co edges, and its rich redox profile make themore »nanosheets both magnetically and electrochemically active, as revealed by solid state magnetic and cyclic voltammetry studies. The length and flexibility of the ditopic linker was varied, and found to have a secondary effect on the structure and stacking of the nanosheets within the 3D crystals. With these results we introduce a deterministic and versatile synthetic entry to programmable functionality and symmetry in 2D superatomic crystals.« less
  5. Nojiri, Hideaki (Ed.)
    ABSTRACT Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at, wheremore »users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.« less