Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Preliminary crystallographic studies of BRCA1 BRCT-ABRAXAS complex.

ABSTRACT: The BRCA1 holoenzyme complex plays an important role in DNA damage repair. ABRAXAS is a newly discovered component of this complex and its C-terminal region directly binds to the BRCA1 BRCT domain. Single crystals of the BRCA1 BRCT-ABRAXAS complex grown by co-crystallization belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 187.18, c = 85.31 Å. Diffraction data were collected on the BM-14 beamline at the ESRF. Molecular-replacement calculations using Phaser led to three molecules in the asymmetric unit and a high solvent content of 76%.

SUBMITTER: Badgujar DC

PROVIDER: S-EPMC3855730 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Preliminary crystallographic studies of BRCA1 BRCT-ABRAXAS complex.

Badgujar Dilip C DC Sawant Ulka U Yadav Lumbini L Hosur M V MV Varma Ashok K AK

Acta crystallographica. Section F, Structural biology and crystallization communications 20131129 Pt 12

The BRCA1 holoenzyme complex plays an important role in DNA damage repair. ABRAXAS is a newly discovered component of this complex and its C-terminal region directly binds to the BRCA1 BRCT domain. Single crystals of the BRCA1 BRCT-ABRAXAS complex grown by co-crystallization belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 187.18, c = 85.31 Å. Diffraction data were collected on the BM-14 beamline at the ESRF. Molecular-replacement calculations using Phaser led to three molec ...[more]

PMID: 24316840

Similar Datasets

Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.

Project description:BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR.

| S-EPMC4747905 | biostudies-literature

Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response.

Project description:The BRCT repeats of the breast and ovarian cancer predisposition protein BRCA1 are essential for tumor suppression. Phosphopeptide affinity proteomic analysis identified a protein, Abraxas, that directly binds the BRCA1 BRCT repeats through a phospho-Ser-X-X-Phe motif. Abraxas binds BRCA1 to the mutual exclusion of BACH1 (BRCA1-associated C-terminal helicase) and CtIP (CtBP-interacting protein), forming a third type of BRCA1 complex. Abraxas recruits the ubiquitin-interacting motif (UIM)-containing protein RAP80 to BRCA1. Both Abraxas and RAP80 were required for DNA damage resistance, G(2)-M checkpoint control, and DNA repair. RAP80 was required for optimal accumulation of BRCA1 on damaged DNA (foci) in response to ionizing radiation, and the UIM domains alone were capable of foci formation. The RAP80-Abraxas complex may help recruit BRCA1 to DNA damage sites in part through recognition of ubiquitinated proteins.

| S-EPMC3573690 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of transglutaminase 2 in complex with Ca2+.

Project description:Transglutaminase 2 (TG2) is a multi-functional protein that has been implicated in a variety of physiological cellular activities, including apoptosis, angiogenesis and cellular differentiation. Two functions of TG2 are protein cross-linking and GTP hydrolysis activities. The protein cross-linking activity of TG2 is positively controlled by calcium; however, the molecular mechanism of its Ca(2+)-dependent activity is completely unknown. In the present study, full-length human TG2 in complex with Ca(2+) was overexpressed, purified and crystallized at 20°C as a first step towards elucidating this mechanism. X-ray diffraction data were collected to a resolution of 3.4 Å from a crystal belonging to space group C2221, with unit-cell parameters a = 133.08, b = 216.30, c = 166.26 Å. Based on these data, the asymmetric unit was estimated to contain three molecules.

| S-EPMC3976076 | biostudies-literature

Purification, crystallization and preliminary crystallographic studies of SPCI-chymotrypsin complex at 2.8 A resolution.

Project description:A binary complex of the Schizolobium parahyba chymotrypsin inhibitor (SPCI) with chymotrypsin was purified by size-exclusion chromatography and crystallized by the sitting-drop vapour-diffusion method with 100 mM MES-NaOH pH 5.5, 20%(w/v) PEG 6000, 200 mM LiCl as precipitant and 200 mM nondetergent sulfobetaine molecular weight 201 Da (NDSB-201) as an additive. SPCI is a small protein with 180 amino-acid residues isolated from S. parahyba seeds and is able to inhibit chymotrypsin at a 1:1 molar ratio by forming a stable complex. X-ray data were collected to 2.8 A resolution from a single crystal of the SPCI-chymotrypsin binary complex under cryogenic conditions. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 45.28, b = 64.57, c = 169.23 A, and the R(merge) is 0.122 for 11 254 unique reflections. A molecular-replacement solution was found using the preliminary crystal structure of SPCI and the structure of chymotrypsin (PDB code 4cha) independently as search models.

| S-EPMC2564883 | biostudies-literature

Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I molecule.

Project description:In order to understand the biological properties of the immune systems of waterfowl and to establish a system for structural studies of duck class I major histocompatibility complex (DuMHC I), a complex of DuMHC I with duck beta(2)-microglobulin (Dubeta(2)m) and the peptide AEIEDLIF (AF8) derived from H5N1 NP residues 251-258 was assembled. The complex was crystallized; the crystals belonged to space group C222(1), with unit-cell parameters a = 54.7, b = 72.4, c = 102.2 A, and diffracted to 2.3 A resolution. Matthews coefficient calculation and initial structure determination by molecular replacement showed that the crystals did not contain the whole DuMHC I complex, but instead contained the DuMHC I alpha3 domain and a Dubeta2m molecule (DuMHC I alpha3+beta2m). Another complex of DuMHC I with the peptide IDWFDGKE derived from a chicken fusion protein also generated the same results. The stable structure of DuMHC I alpha3+beta2m may reflect some unique characteristics of DuMHC I and pave the way for novel MHC structure-related studies in the future.

| S-EPMC2805548 | biostudies-literature

Complex assembly, crystallization and preliminary X-ray crystallographic studies of the swine major histocompatibility complex molecule SLA-1*1502.

Project description:In order to illustrate the structure of the swine MHC class I (SLA-I) molecule and to evaluate the cytotoxic T lymphocyte (CTL) response against porcine reproductive and respiratory syndrome virus (PRRSV), the ternary complex of the SLA-I molecule termed SLA-1*1502 with ?(2)-microglobulin and the CTL epitope TMPPGFELY (PRRSV-NSP9(TY9)) derived from PRRSV nonstructural protein 9 (residues 198-206) was assembled and crystallized. The crystal diffracted X-rays to 2.2 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 66.1, b = 74.1, c = 98.6 Å; it contained one molecule in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.74 Å(3) Da(-1) and 55.17%, respectively. The results will be helpful in obtaining insight into the structural basis of the presentation of viral epitopes by SLA-I.

| S-EPMC3087642 | biostudies-literature

Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage.

Project description:The Brca1 A complex contains Brca1/Bard1, Abraxas, Rap80, and Brcc36; however, with the exception of the Brca1-Abraxas interaction, how the A complex is assembled is not known. The A complex is localized to sites of DNA damage through the UIM domains of RAP80, which bind K63-linked polyubiquitin chains. In this study, we identified an FHA domain RING finger E3 ubiquitin ligase, RNF8, and an E2-conjugating enzyme known to form K63-polyubiquitin chains, Ubc13, each of which is required to recruit the Brca1 A complex to sites of DNA damage. Rnf8 localizes to sites of DNA damage through an FHA-domain-containing region. We found that Rap80 contains an Abraxas interaction domain [AIR (Abraxas-interacting region)], required for association of Rap80 with Abraxas, Brca1, and Brcc36. Abraxas and Brcc36 associate through coiled-coil domains on each protein. These data suggest a model through which Ubc13 and Rnf8 are recruited to sites of DNA damage through DNA-damage-induced phosphorylation of a chromatin-associated protein and generate polyubiquitin chains that then recruit Rap80 and the entire Brca1 A complex to DNA-damage foci. This sequential E3 ubiquitin ligase recruitment constitutes a ubiquitin ligase cascade required for DNA repair and checkpoint signaling.

| S-EPMC2410075 | biostudies-literature

Crystallization and preliminary crystallographic studies of Helicobacter pylori arginase.

Project description:Helicobacter pylori arginase is an important factor in evasion of the host's immune system and contributes to persistent infection by this bacterium. It is unique in many aspects compared with other arginases: for example, it has optimal activity with Co(2+) as a cofactor rather than Mn(2+) and has strongest activity at acidic pH instead of alkaline pH. In this study, H. pylori arginase was purified and crystallized in complex with Mn(2+) and a diffraction data set was collected to 2.2 Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 94.69, b = 102.24, c = 148.61 Å.

| S-EPMC3107149 | biostudies-literature

Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin.

Project description:Room-temperature and 100 K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7 A resolution using a home source, to 1.6 A resolution on NE-CAT at the Advanced Photon Source and to 2.0 A resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from this site in the low-temperature structure.

| S-EPMC2852348 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of swine CD8?.

Project description:CD8?? homodimers or CD8?? heterodimers form on the T-cell surface, where they are essential as co-receptors for MHC class I molecules in activation of the CTL response. To date, swine have been found to show the highest percentage of lymphocytes with surface expression of CD8?. Crystallographic analysis of swine CD8? (sCD8?) to 1.8?Å resolution revealed that the crystals belonged to space group P3(2)21, with unit-cell parameters a = 80.97, b = 80.97, c = 95.19?Å. The Matthews coefficient and the solvent content were calculated to be 3.23?Å(3)?Da(-1) and 61.89%, respectively. These results may aid further structural and functional analyses of sCD8?.

| S-EPMC3151120 | 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