Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structure of d(CCCCGGTACCGGGG)2 at 1.65?A resolution.

ABSTRACT: The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5?Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65?Å in space group P4?2?2. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. This structure allowed the unambiguous identification of solvent interactions.

SUBMITTER: Purushothaman M

PROVIDER: S-EPMC4089521 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structure of d(CCCCGGTACCGGGG)2 at 1.65 Å resolution.

Purushothaman Monica M Varghese Anna A Mandal Pradeep Kumar PK Gautham Namasivayam N

Acta crystallographica. Section F, Structural biology communications 20140618 Pt 7

The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5 Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65 Å in space group P4₁2₁2. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. ...[more]

PMID: 25005078

Similar Datasets

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 A resolution.

Project description:Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 A using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005), FEBS J. 272, 6067-6076]. In this communication of parallel studies, BAL was crystallized in an alternative space group (P2(1)2(1)2(1)) and its structure refined to a resolution of 1.65 A, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.

| S-EPMC2335142 | biostudies-literature

Structure of the Yersinia pestis tip protein LcrV refined to 1.65 A resolution.

Project description:The human pathogen Yersinia pestis requires the assembly of the type III secretion system (T3SS) for virulence. The structural component of the T3SS contains an external needle and a tip complex, which is formed by LcrV in Y. pestis. The structure of an LcrV triple mutant (K40A/D41A/K42A) in a C273S background has previously been reported to 2.2 Å resolution. Here, the crystal structure of LcrV without the triple mutation in a C273S background is reported at a higher resolution of 1.65 Å. Overall the two structures are similar, but there are also notable differences, particularly near the site of the triple mutation. The refined structure revealed a slight shift in the backbone positions of residues Gly28-Asn43 and displayed electron density in the loop region consisting of residues Ile46-Val63, which was disordered in the original structure. In addition, the helical turn region spanning residues Tyr77-Gln95 adopts a different orientation.

| S-EPMC3660882 | biostudies-literature

1.65 A resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae.

Project description:ToxT is an AraC-family transcriptional activator protein that controls the expression of key virulence factors in Vibrio cholerae, the causative agent of cholera. ToxT directly activates the expression of the genes that encode the toxin-coregulated pilus and cholera toxin, and also positively auto-regulates its own expression from the tcp promoter. The crystal structure of ToxT has previously been solved at 1.9 Å resolution (PDB entry 3gbg). In this study, a crystal structure of ToxT at 1.65 Å resolution with a similar overall structure to the previously determined structure is reported. However, there are distinct differences between the two structures, particularly in the region that extends from Asp101 to Glu110. This region, which can influence ToxT activity but was disordered in the previous structure, can be traced entirely in the current structure.

| S-EPMC5012214 | biostudies-literature

Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 A resolution.

Project description:Chemotherapeutic alkylating agents, such as bifunctional nitrogen mustards and cisplatins, generate interstrand DNA cross-links that inhibit cell proliferation by arresting DNA transcription and replication. A synthetic N4C-ethyl-N4C interstrand cross-link between opposing cytidines mimics the DNA damage produced by this class of clinically important compounds and can be synthesized in large quantities to study the repair, physical properties, and structures of these DNA adducts. The X-ray structure of a DNA duplex d(CCAAC*GTTGG)2 containing a synthetic N4C-ethyl-N4C interstrand cross-link between the cytosines of the central CpG step (*) has been determined at 1.65 A resolution. This structure reveals that the ethyl cross-link in the CpG major groove does not significantly disrupt the B-form DNA helix. Comparison of the N4C-ethyl-N4C cross-linked structure with the structure of an un-cross-linked oligonucleotide of the same sequence reveals that the cross-link selectively stabilizes a preexisting alternative conformation. The conformation preferred by the cross-linked DNA is constrained by the geometry of the ethyl group bridging the cytosine amines. Characteristics of the cross-linked CpG step include subtle differences in the roll of the base pairs, optimized Watson-Crick hydrogen bonds, and loss of a divalent cation binding site. Given that the N4C-ethyl-N4C cross-link stabilizes a preexisting conformation of the CpG step, this synthetically accessible substrate presents an ideal model system for studying the genomic effects of covalently coupling the DNA strands, independent of gross alterations in DNA structure.

| S-EPMC2625308 | biostudies-literature

New protein fold revealed by a 1.65 A resolution crystal structure of Francisella tularensis pathogenicity island protein IglC.

Project description:Francisella tularensis is a highly infectious Gram-negative intracellular pathogen that causes the fulminating disease tularemia and is considered to be a potential bioweapon. F. tularensis pathogenicity island proteins play a key role in modulating phagosome biogenesis and subsequent bacterial escape into the cytoplasm of macrophages. The 23 kDa pathogenicity island protein IglC is essential for the survival and proliferation of F. tularensis in macrophages. Seeking to gain some insight into its function, we determined the crystal structure of IglC at 1.65 A resolution. IglC adopts a beta-sandwich conformation that exhibits no similarity with any known protein structure.

| S-EPMC2211698 | biostudies-literature

High resolution structure of hs21

Project description:Here we attempt to describe the structure of Hs21 at high resolution using proximity ligation assays in combination with target enrichment in several conditions (yet to be determined). We will also generate additional epigenetic information that will help with the interpretation of the data.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-04-08 | E-ERAD-349 | biostudies-arrayexpress

K(1.65)V(1.78)W(0.22)O(2)(AsO(4))(2).

Project description:The title potassium vanadium tungsten bis-(arsenate oxide) was synthesized by a solid-state reaction at 973?K. The crystal structure is isotypic with KVOPO(4) and contains a [MVAs(2)O(10)](?) framework built up from single MO(6) (M = V+W) octa-hedra sharing corners with single VO(6) octa-hedra and AsO(4) tetra-hedra. This structure shows the existence of infinite [VAsO(8)](?) and [MAsO(8)](?) chains running along the a and c directions, respectively. All atoms are located on general positions. The metal position M is statistically occupied by 78% V and 22% W.

| S-EPMC2970124 | biostudies-literature

Atomic resolution structure of apoferritin

Project description: Not available

| EMPIAR-10424 | biostudies-other

Low-resolution structure of Drosophila translin.

Project description:Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to R work (R free) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin-TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers.

| S-EPMC3642112 | biostudies-literature

High-resolution analysis of chromatin structure by Mnase-SSP

Project description:Proof-of-concept for Mnase-SSP: a variant of Mnase-seq. Mnase-SSP dramatically increases the representation of short fragments of nucleolytically-digested DNA, enabling simultaneous analysis of transcription factor binding and nucleosome occupancy using the same assay. We used MNase-SSP to demarcate chromatin architecture at murine promoters and at transcription factor binding sites in murine embryonic stem cells. Are results reveal heterogeneity in the binding mode of C2H2 zinc fingers like Ctcf and Rest, demonstrating that Mnase-SSP, and SSP in general, as a flexible platform for profiling nucleolytically digested DNA for MNase-seq, MNase-ChIP, or CUT&RUN with reduced bias.

2019-02-12 | GSE125053 | GEO

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