scholarly journals Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation

IUCrJ ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 238-256
Author(s):  
Mariusz Jaskolski ◽  
Zbigniew Dauter ◽  
Ivan G. Shabalin ◽  
Miroslaw Gilski ◽  
Dariusz Brzezinski ◽  
...  

The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CLpro, an important target for the design of drugs against COVID-19. The structures of the unliganded enzyme and its complexes with a number of inhibitors were determined by multiple research groups using different experimental approaches and conditions; the resulting structures span 13 different polymorphs representing seven space groups. The structures of the enzyme itself, all determined by molecular replacement, are highly similar, with the exception of one polymorph with a different inter-domain orientation. However, a number of complexes with bound inhibitors were found to pose significant problems. Some of these could be traced to faulty definitions of geometrical restraints for ligands and to the general problem of a lack of such information in the PDB depositions. Several problems with ligand definition in the PDB itself were also noted. In several cases extensive corrections to the models were necessary to adhere to the evidence of the electron-density maps. Taken together, this analysis of a large number of structures of a single, medically important protein, all determined within less than a year using modern experimental tools, should be useful in future studies of other systems of high interest to the biomedical community.

2015 ◽  
Vol 71 (2) ◽  
pp. 186-194 ◽  
Author(s):  
G. Chirikjian ◽  
S. Sajjadi ◽  
D. Toptygin ◽  
Y. Yan

The main goal of molecular replacement in macromolecular crystallography is to find the appropriate rigid-body transformations that situate identical copies of model proteins in the crystallographic unit cell. The search for such transformations can be thought of as taking place in the coset space Γ\Gwhere Γ is the Sohncke group of the macromolecular crystal andGis the continuous group of rigid-body motions in Euclidean space. This paper, the third in a series, is concerned with viewing nonsymmorphic Γ in a new way. These space groups, rather than symmorphic ones, are the most common ones for protein crystals. Moreover, their properties impact the structure of the space Γ\G. In particular, nonsymmorphic space groups contain both Bieberbach subgroups and symmorphic subgroups. A number of new theorems focusing on these subgroups are proven, and it is shown that these concepts are related to the preferences that proteins have for crystallizing in different space groups, as observed in the Protein Data Bank.


2005 ◽  
Vol 38 (5) ◽  
pp. 808-818 ◽  
Author(s):  
David W. Ritchie

Analytic expressions are presented for calculating translations of high-order three-dimensional expansions of orthonormal real spherical harmonic and Gaussian-type or exponential-type radial basis functions. When used with real spherical harmonic rotation matrices, the resulting translation matrices provide a fully analytic method of calculating six-dimensional real-space rotational–translational correlations. The correlation algorithm is demonstrated by using an exhaustive search to superpose the steric density functions of a pair of similar globular proteins in a matter of seconds on a contemporary personal computer. It is proposed that the techniques described could be used to accelerate the calculation ofe.g.real-space electron density correlations in molecular replacement, docking proteins into electron microscopy density maps, and searching the Protein Data Bank for structural homologues.


2021 ◽  
Author(s):  
Lawrence Chai ◽  
Ping Zhu ◽  
Jin Chai ◽  
Changxu Pang ◽  
Babak Andi ◽  
...  

AbstractCrystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a dominant phasing method for the crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database for finding suitable templates for phasing. However, such sequence information is not always available such as when proteins are crystallized with unknown binding partner proteins or when the crystal is that of a contaminant. The recent development of AlphaFold has resulted in the availability of predicted protein structures for all proteins from twenty species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough for sequence-independent phasing of diffraction data from two crystallization contaminants for which we had not identified the protein. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained which allowed the identification and structure determination of both structures, YncE and YadF. Our results advocate a general utility of AlphaFold-predicted structure database with respect to crystallographic phasing.


Crystals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1227
Author(s):  
Lawrence Chai ◽  
Ping Zhu ◽  
Jin Chai ◽  
Changxu Pang ◽  
Babak Andi ◽  
...  

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.


Author(s):  
T. Y. Tan ◽  
W. K. Tice

In studying ion implanted semiconductors and fast neutron irradiated metals, the need for characterizing small dislocation loops having diameters of a few hundred angstrom units usually arises. The weak beam imaging method is a powerful technique for analyzing these loops. Because of the large reduction in stacking fault (SF) fringe spacing at large sg, this method allows for a rapid determination of whether the loop is faulted, and, hence, whether it is a perfect or a Frank partial loop. This method was first used by Bicknell to image small faulted loops in boron implanted silicon. He explained the fringe spacing by kinematical theory, i.e., ≃l/(Sg) in the fault fringe in depth oscillation. The fault image contrast formation mechanism is, however, really more complicated.


Author(s):  
D.J. Eaglesham

Convergent Beam Electron Diffraction is now almost routinely used in the determination of the point- and space-groups of crystalline samples. In addition to its small-probe capability, CBED is also postulated to be more sensitive than X-ray diffraction in determining crystal symmetries. Multiple diffraction is phase-sensitive, so that the distinction between centro- and non-centro-symmetric space groups should be trivial in CBED: in addition, the stronger scattering of electrons may give a general increase in sensitivity to small atomic displacements. However, the sensitivity of CBED symmetry to the crystal point group has rarely been quantified, and CBED is also subject to symmetry-breaking due to local strains and inhomogeneities. The purpose of this paper is to classify the various types of symmetry-breaking, present calculations of the sensitivity, and illustrate symmetry-breaking by surface strains.CBED symmetry determinations usually proceed by determining the diffraction group along various zone axes, and hence finding the point group. The diffraction group can be found using either the intensity distribution in the discs


2017 ◽  
Vol 45 (2) ◽  
pp. 455-464
Author(s):  
T.T. Xue ◽  
J. Liu ◽  
Y.B. Shen ◽  
G.Q. Liu

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