Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7.

ABSTRACT: Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to approximately 3.0 A resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 A in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R(merge) of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.

SUBMITTER: Quesada O

PROVIDER: S-EPMC2344100 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7.

Quesada Odayme O Gurda Brittney B Govindasamy Lakshmanan L McKenna Robert R Kohlbrenner Erik E Aslanidi George G Zolotukhin Sergei S Muzyczka Nicholas N Agbandje-McKenna Mavis M

Acta crystallographica. Section F, Structural biology and crystallization communications 20071130 Pt 12

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to approximately 3.0 A resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 A in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R(merge) of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axi ...[more]

PMID: 18084098

Similar Datasets

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 9.

Project description:Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P3(2), with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetric unit capsid have been determined by molecular-replacement methods and structure determination is in progress.

| S-EPMC2705643 | biostudies-literature

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1.

Project description:Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 A, alpha = 62.3 degrees) and shown to diffract X-rays to at least 2.5 A resolution. The diffraction data were subsequently processed and reduced with an overall R(sym) of 12.3% and a completeness of 89.0%. Based on the unit-cell volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 A resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.

| S-EPMC2225374 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain.

Project description:Drep2 is a novel nuclease from the fruit fly that might have a similar function in apoptosis to DFF40 and DFF45, which are primary players in apoptotic DNA fragmentation. Drep2 contains a conserved CIDE domain of ?90 amino-acid residues that is involved in protein-protein interaction. In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3?Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37?Å.

| S-EPMC4188092 | biostudies-literature

Expression, purification and preliminary X-ray crystallographic studies of the human immunodeficiency virus 1 subtype C protease.

Project description:Crystals of the human immunodeficiency virus 1 (HIV-1) subtype C protease (PR) complexed with the clinically used inhibitors indinavir (IDV) and nelfinavir (NFV) have been grown in the monoclinic space group P2(1), with mean unit-cell parameters a = 46.7 (+/-0.1), b = 59.8 (+/-0.3), c = 87.0 (+/-0.4) A, beta = 95.2 (+/-0.5) degrees. The crystals of both complexes have been shown to diffract X-rays to 2.3 A resolution. The diffraction data for the subtype C PR complexes with IDV and NFV were subsequently processed and reduced, with overall R(sym) values of 8.4 and 11.4%, respectively. Based on the unit-cell volumes, molecular-replacement results and packing considerations, there are two protease homodimers per crystallographic asymmetric unit in each of the complexes. The data were initially phased using a model based on the crystal structure of HIV-1 subtype B PR; the structures have been determined and further refinement and analysis are in progress. These structures and subsequent studies with other inhibitors will greatly aid in correlating the amino-acid variation between the different HIV PRs and understanding their differential sensitivity and resistance to current drug therapy.

| S-EPMC2330223 | biostudies-literature

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D.

Project description:Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D_HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D_HCR was obtained. The recombinant BoNT/D_HCR was crystallized and the crystals diffracted to 1.65?Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=60.8, b=89.7, c=93.9?Å. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

| S-EPMC2998366 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis.

Project description:The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6122 or P6522, with unit-cell parameters a = b = 198.0, c = 364.1?Å, ? = ? = 90, ? = 120°, and diffracted to a resolution of 3.3?Å.

| S-EPMC4118811 | biostudies-literature

Purification, crystallization and preliminary x-ray crystallographic studies of RAIDD Death-Domain (DD).

Project description:Caspase-2 activation by formation of PIDDosome is critical for genotoxic stress induced apoptosis. PIDDosome is composed of three proteins, RAIDD, PIDD, and Caspase-2. RAIDD is an adaptor protein containing an N-terminal Caspase-Recruiting-Domain (CARD) and a C-terminal Death-Domain (DD). Its interactions with Caspase-2 and PIDD through CARD and DD respectively and formation of PIDDosome are important for the activation of Caspase-2. RAIDD DD cloned into pET26b vector was expressed in E. coli cells and purified by nickel affinity chromatography and gel filtration. Although it has been known that the most DDs are not soluble in physiological condition, RAIDD DD was soluble and interacts tightly with PIDD DD in physiological condition. The purified RAIDD DD alone has been crystallized. Crystals are trigonal and belong to space group P3(1)21 (or its enantiomorph P3(2)21) with unit-cell parameters a = 56.3, b = 56.3, c = 64.9 A and gamma = 120 degrees . The crystals were obtained at room temperature and diffracted to 2.0 A resolution.

| S-EPMC2705503 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3899c from Mycobacterium tuberculosis.

Project description:Rv3899c, a hypothetical protein from Mycobacterium tuberculosis that is conserved within the mycobacteria, is predicted to be secreted and has been found in culture filtrates. Here, Rv3899c has been cloned, expressed in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion method with PEG 3350 as a precipitant was used to crystallize the protein. N-terminal sequencing results showed that the amino-acid sequence of the crystallized protein began with GATAG, indicating that it is a fragment containing residues 184-410 of Rv3899c. Rv3899c184-410 crystals exhibited the symmetry of space group P2(1)2(1)2(1), with unit-cell parameters a=49.88, b=54.72, c=75.52?Å, ?=?=?=90°, and diffracted to a resolution of 1.90?Å.

| S-EPMC4304759 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray crystallographic studies of Deinococcus radiodurans thioredoxin reductase.

Project description:Deinococcus radiodurans, a Gram-positive bacterium capable of withstanding extreme ionizing radiation, contains two thioredoxins (Trx and Trx1) and a single thioredoxin reductase (TrxR) as part of its response to oxidative stress. Thioredoxin reductase is a member of the family of pyridine nucleotide-disulfide oxidoreductase flavoenzymes. Recombinant D. radiodurans TrxR with a His tag at the N-terminus was expressed in Escherichia coli and purified by metal-affinity chromatography. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of 35% PEG 4000, 0.2 M ammonium acetate and citric acid buffer pH 5.1 at 293 K. X-ray diffraction data were collected on a cryocooled crystal to a resolution of 1.9 angstroms using a synchrotron-radiation source. The space group was determined to be P3(2)21, with unit-cell parameters a = b = 84.33, c = 159.88 angstroms. The structure of the enzyme has been solved by molecular-replacement methods and structure refinement is in progress.

| S-EPMC2242918 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic studies of the Mycobacterium tuberculosis DNA gyrase CTD.

Project description:Mycobacterium tuberculosis DNA gyrase, a nanomachine involved in regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target of fluoroquinolone in the treatment of tuberculosis. The C-terminal domain (CTD) of the DNA gyrase A subunit possesses a unique feature, the ability to wrap DNA in a chiral manner, that plays an essential role during the catalytic cycle. A construct of 36 kDa corresponding to this domain has been overproduced, purified and crystallized. Diffraction data were collected to 1.55 Å resolution. Cleavage of the N-terminal His tag was crucial for obtaining crystals. The crystals belonged to space group P2(1)2(1)2(1), with one molecule in the asymmetric unit and a low solvent content (33%). This is the first report of the crystallization and preliminary X-ray diffraction studies of a DNA gyrase CTD from a species that contains one unique type II topoisomerase.

| S-EPMC3274397 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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