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Coronaviruses (2020)
Structural biology has an important role in fighting the current COVID-19 pandemic caused by the coronavirus known as SARS-CoV-2. This virtual issue presents articles and abstracts on coronaviruses that have been published in IUCr journals.
Many structural biology initiatives are under way to combat COVID-19 and here are just a few examples: a giant fragment screening exercise led by researchers at Diamond Light Source (https://covid.postera.ai/covid); the CASP initiative to model SARS-2-CoV targets (http://predictioncenter.org/caspcommons/index.cgi); a protopedia page on COVID-19 [http://proteopedia.org/w/Coronavirus_Disease_2019_(COVID-19)]; a large collaborative effort on rerefined structures with a webpage featuring numerous links (https://github.com/thorn-lab/coronavirus_structural_task_force); the COVID-19 Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data (https://www.ebi.ac.uk/covid-19).
Cover illustration: This scanning electron microscope image shows SARS-CoV-2 (yellow) - the virus that causes COVID-19 - isolated from a patient in the USA, emerging from the surface of cells (pink) cultured in the laboratory. Credit: NIAID-RML
editorial
The application of cryo-EM methods to study SARS-CoV-2 proteins provides a convincing demonstration of the power of cryo-EM in the arsenal of structural biology.
Crystallography in its broadest sense has a crucial role to play in addressing the current COVID-19 pandemic. An outpouring of structural information on key viral proteins has resulted and importantly these data have immediately been shared with researchers round the world to speed the discovery of effective therapeutic agents.
research articles
The X-ray structure and SAXS analysis of the C-terminal domain of the nucleocapsid from Middle East respiratory syndrome coronavirus, an emerging virus, are reported.
PDB reference: C-terminal domain of MERS-CoV nucleocapsid, 6g13
The structure of interferon-stimulated gene product 15 (ISG15) from the bat species M. davidii was elucidated to 1.37 Å resolution. Structural comparison of this ISG15 originating from a species of vesper bat endemic to China with those from mouse and human illuminates a conserved hydrophobic interface between the ubiquitin-like domains of ISG15. The importance of this interaction was probed for its influence on ISG15 engagement by a papain-like viral deISGylase using isothermal titration calorimetry.
PDB reference: ISG15 from Myotis davidii, 6mdh
Open 
access
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The complete post-fusion core structure of the Human coronavirus 229E spike protein was determined at 1.86 Å resolution. Comparison of the interactions between heptad repeats HR1 and HR2 in different human coronaviruses reveals some differences, which should be taken into consideration when designing pan-coronavirus HR2-mimicking inhibitors that target HR1.
PDB reference: HCoV-229E fusion core, 5yl9
The structural characterization of the N-terminal part of the nucleocapsid from Middle East respiratory syndrome coronavirus (MERS-CoV), a recently emerging virus, is reported. The structure of the N-terminal region, which includes a disordered tail followed by a globular domain, was obtained by combining X-ray diffraction and SAXS.
PDB reference: N-terminal domain of the MERS-CoV nucleocapsid, 4ud1
Crystals of the N-terminal domain of the nucleocapsid protein from Middle East respiratory syndrome coronavirus that diffracted X-rays to a resolution of at least 2.63 Å are described.
This article describes preliminary crystallographic data for the I26A/N52A mutant of nonstructural protein 15 from Human coronavirus 229E.
MERS-CoV 3CLpro has been crystallized and X-ray crystal structures have been solved in three different crystal forms representing the free enzyme structure and the enzyme–product complex.
This article describes preliminary crystallographic data of a complex consisting of human coronavirus NL63 main protease and its inhibitor N3.
The crystal structure of the papain-like protease (PLpro) C112S mutant in complex with ubiquitin offers insight into the molecular basis of the catalytic mechanism of PLpro and its substrate binding. An N-cyclohexyl-2-aminethanesulfonic acid molecule in the active site suggests a possible approach to inhibition.
PDB reference: PLpro C112S mutant, complex with ubiquitin, 4m0w
This article describes the preliminary crystallographic data of a functional mutant (N60K) of nonstructural protein 9 from Human coronavirus HKU1.
The crystal structure of the dimeric R298A mutant of SARS-CoV Mpro offers insights into the molecular mechanism controlling monomer–dimer conversion during the process of Mpro maturation.
PDB reference: SARS-CoV Mpro, R298A mutant, 4hi3
The expression, purification and crystallization of the SARS coronavirus nsp16 RNA-cap AdoMet-dependent (nucleoside-2′O)-methyltransferase in complex with its activating factor nsp10 are reported.
The C-terminal domain of SARS coronavirus nonstructural protein 2 was cloned, overexpressed, purified and crystallized; the crystals diffracted to 2.5 Å resolution.
Crystals of the N-terminal domain of nucleocapsid protein from human coronavirus OC43 were obtained that diffracted X-rays to a resolution of at least 1.7 Å.
The gene segment encoding avian infectious bronchitis virus nonstructural protein 9 has been cloned and expressed in Escherichia coli. The protein has been crystallized and the crystals diffracted X-rays to 2.44 Å resolution.
Open access
access
The structure of the cytosolic C-terminal domain of nonstructural protein 4 from feline coronavirus has been determined and analyzed.
PDB reference: C-terminal domain of nsp4, 3gzf, r3gzfsf
The structure of the X (ADRP) domain of nonstructural protein 3 from feline coronavirus has been determined in two crystal forms. The binding of glycerol-3-phosphate and ADP-ribose is described.
The gene that encodes human coronavirus HKU1 nonstructural protein 9 was cloned and expressed in Escherichia coli and the protein was subjected to crystallization trials.
Free
The severe acute respiratory syndrome (SARS) coronavirus outbreak in 2003 had profound social and economic impacts worldwide. This review highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.
The three-dimensional structure of a SARS coronavirus-derived peptide, VQQESSFVM, bound to the human major histocompatibility complex (MHC) class I antigen HLA-B*1501 is presented.
PDB reference: HLA-B*1501–VQQESSFVM complex, 3c9n, r3c9nsf
The avian infectious bronchitis virus main protease has been crystallized; crystals diffract to 2.7 Å resolution.
Crystals of Nsp15 from the aetiological agent of SARS have been grown at room temperature. Crystals have cubic symmetry and diffract to a maximum resolution of 2.7 Å.
The SARS-CoV macro domain was expressed, purified and crystallized. Selenomethionine-labelled crystals diffracted to 1.8 Å resolution.
An orthorhombic crystal form of the SARS CoV main proteinase diffracting to a resolution of 1.9 Å is reported. The conformation of residues in the catalytic site indicates an active enzyme.
PDB reference: SARS coronavirus main proteinase, 2c3s, 2c3ssf
Crystals of the fusion core of SARS-CoV spike protein have been grown at 291 K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.8 Å resolution at 100 K in-house. The crystals have unit-cell parameters a = 121.2, b = 66.3, c = 70.0 Å, α = γ = 90, β = 107.4° and belong to space group C2.
Open access
access
Preliminary crystallographic data of the fusion core of the spike protein of the murine coronavirus mouse hepatitis virus have been obtained.
A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. Here, the cloning, E. coli expression, purification, and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported.
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