Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Surprises and pitfalls arising from (pseudo)symmetry.

ABSTRACT: It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

SUBMITTER: Zwart PH

PROVIDER: S-EPMC2394827 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Surprises and pitfalls arising from (pseudo)symmetry.

Zwart Peter H PH Grosse-Kunstleve Ralf W RW Lebedev Andrey A AA Murshudov Garib N GN Adams Paul D PD

Acta crystallographica. Section D, Biological crystallography 20071205 Pt 1

It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new ...[more]

PMID: 18094473

Similar Datasets

Pseudo-heterolepticity in Low-Symmetry Metal-Organic Cages.

Project description:Heteroleptic metal-organic cages, formed through integrative self-assembly of ligand mixtures, are highly attractive as reduced symmetry supramolecular hosts. Ensuring high-fidelity, non-statistical self-assembly, however, presents a significant challenge in molecular engineering due to the inherent difficulty in predicting thermodynamic energy landscapes. In this work, two conceptual strategies are described that circumvent this issue, using ligand design strategies to access structurally sophisticated metal-organic hosts. Using these approaches, it was possible to realise cavity environments described by two inequivalent, unsymmetrical ligand frameworks, representing a significant step forward in the construction of highly anisotropic confined spaces.

| S-EPMC9828238 | biostudies-literature

Anterior mitral line pseudo-block: Pitfalls of the atrial differential pacing maneuver.

Project description: Not available

| S-EPMC9795285 | biostudies-literature

c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.

Project description:The ydaO riboswitch, involved in sporulation, osmotic stress responses and cell wall metabolism, targets the second messenger cyclic-di-AMP with subnanomolar affinity. We have solved the structure of c-di-AMP bound to the Thermoanaerobacter tengcongensis ydaO riboswitch, thereby identifying a five-helical scaffold containing a zippered-up bubble, a pseudoknot and long-range tertiary base pairs. Highlights include the identification of two c-di-AMP binding pockets on the same face of the riboswitch, related by pseudo-two-fold symmetry, with potential for cross-talk between sites mediated by adjacently positioned base-stacking alignments connecting pockets. The adenine rings of bound c-di-AMP molecules are wedged between bases and stabilized by stacking, base-sugar and sugar-sugar intermolecular hydrogen bonding interactions. The structural studies are complemented by isothermal titration calorimetry-based binding studies of mutants mediating key tertiary intermolecular contacts. The T. tengcongensis ydaO riboswitch, like its Bacillus subtilis counterpart, most likely functions through a transcription termination mechanism, with the c-di-AMP bound state representing an 'off' switch.

| S-EPMC4217635 | biostudies-literature

The phase transitions of 4-aminopyridine-based indolocarbazoles: twinning, local- and pseudo-symmetry.

Project description:The phase transitions and polymorphism of three 4-aminopyridine-based indolocarbazole analogues are analyzed with respect to symmetry relationships and twinning. Seven polymorphs were structurally characterized using single-crystal diffraction. 5NICz (the indolo[3,2,1-jk]carbazole derivative with the C atom in the 5-position replaced by N) crystallizes as a P21/a high-temperature (270 K) polymorph and as a Pca21 low-temperature (150 K) polymorph. Even though their space-group symmetry is not related by a group-subgroup relationship, the local symmetries of both belong to the same order-disorder (OD) groupoid family. Both are polytypes of a maximum degree of order and are twinned by point operations of the other polytype. 2NICz (C atom in the 2-position replaced by N) likewise crystallizes in a high-temperature (Pcca, 280 K) polymorph and a low-temperature (P21/c, 150 K) polymorph. Here, the space-group symmetries are related by a group-subgroup relationship. The low-temperature phase is twinned by the point operations lost on cooling. The crystal structure of bulk 2,5NICz (N-substitution at the 2- and 5-positions) was unrelated to 2NICz and 5NICz and no phase transition was observed. Isolated single crystals of a different polymorph of 2,5NICz, isotypic with 2NICz, were isolated. However, the analogous phase transition in this case takes place at distinctly higher temperatures (> 300 K).

| S-EPMC6457041 | biostudies-literature

More surprises from Kinetoplastida.

Project description: Not available

| S-EPMC33532 | biostudies-literature

Giant Viruses-Big Surprises.

Project description:Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1 Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant viral proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.

| S-EPMC6563228 | biostudies-literature

Exploiting pseudo C2-symmetry for an efficient synthesis of the F-ring of the spongistatins.

Project description:A concise and efficient synthesis of the F-ring fragment of the potent antimitotic marine macrolide spongistatin 1 has been developed. The key sequence involves double cross-metathesis/Sharpless asymmetric dihydroxylation reactions to establish four stereocenters in a pseudo C2-symmetric array, followed by a selective protection reaction that breaks the pseudosymmetry, establishes a fifth stereocenter, and effectively differentiates the ester termini. Overall, the six contiguous stereocenters in the C(37)-C(45) F-ring fragment are established in just seven steps.

| S-EPMC3845086 | biostudies-literature

Viral noncoding RNAs: more surprises.

Project description:Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles--including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation--have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.

| S-EPMC4378190 | biostudies-literature

Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry.

Project description:Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that synthesize a myriad of diverse molecules. Tailoring domains have been co-opted into NRPSs to introduce further variety into nonribosomal peptide products. Linear gramicidin synthetase contains a unique formylation-tailoring domain in its initiation module (F-A-PCP). The structure of the F-A di-domain has previously been determined in a crystal form which had large solvent channels and no density for the minor Asub subdomain. An attempt was made to take advantage of this packing by removing the Asub subdomain from the construct (F-AΔsub) in order to produce a crystal that could accommodate the PCP domain. In the resulting crystal the original packing network was still present, but a second network with the same packing and almost no contact with the original network took the place of the solvent channels and changed the space group of the crystal.

| S-EPMC5053139 | biostudies-literature

Surprises from an unusual CLC homolog.

Project description:The chloride channel (CLC) family is distinctive in that some members are Cl(-) ion channels and others are Cl(-)/H(+) antiporters. The molecular mechanism that couples H(+) and Cl(-) transport in the antiporters remains unknown. Our characterization of a novel bacterial homolog from Citrobacter koseri, CLC-ck2, has yielded surprising discoveries about the requirements for both Cl(-) and H(+) transport in CLC proteins. First, even though CLC-ck2 lacks conserved amino acids near the Cl(-)-binding sites that are part of the CLC selectivity signature sequence, this protein catalyzes Cl(-) transport, albeit slowly. Ion selectivity in CLC-ck2 is similar to that in CLC-ec1, except that SO(4)(2-) strongly competes with Cl(-) uptake through CLC-ck2 but has no effect on CLC-ec1. Second, and even more surprisingly, CLC-ck2 is a Cl(-)/H(+) antiporter, even though it contains an isoleucine at the Glu(in) position that was previously thought to be a critical part of the H(+) pathway. CLC-ck2 is the first known antiporter that contains a nonpolar residue at this position. Introduction of a glutamate at the Glu(in) site in CLC-ck2 does not increase H(+) flux. Like other CLC antiporters, mutation of the external glutamate gate (Glu(ex)) in CLC-ck2 prevents H(+) flux. Hence, Glu(ex), but not Glu(in), is critical for H(+) permeation in CLC proteins.

| S-EPMC3491686 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data