Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a graphene oxide grid (preferred orientations)

ABSTRACT:

SUBMITTER: Melody Grace Campbell

PROVIDER: EMPIAR-10344 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Cryo-EM Reveals Integrin-Mediated TGF-β Activation without Release from Latent TGF-β.

Campbell Melody G MG Cormier Anthony A Ito Saburo S Seed Robert I RI Bondesson Andrew J AJ Lou Jianlong J Marks James D JD Baron Jody L JL Cheng Yifan Y Nishimura Stephen L SL

Cell 20200116 3

Integrin αvβ8 binds with exquisite specificity to latent transforming growth factor-β (L-TGF-β). This binding is essential for activating L-TGF-β presented by a variety of cell types. Inhibiting αvβ8-mediated TGF-β activation blocks immunosuppressive regulatory T cell differentiation, which is a potential therapeutic strategy in cancer. Using cryo-electron microscopy, structure-guided mutagenesis, and cell-based assays, we reveal the binding interactions between the entire αvβ8 ectodomain and it ...[more]

PMID: 31955848

Similar Datasets

CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a holey carbon grid (strongly preferred orientations)

Project description: Not available

| EMPIAR-10343 | biostudies-other

CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to two Fabs on a holey carbon grid (minimal preferred orientations)

Project description: Not available

| EMPIAR-10345 | biostudies-other

Cryo-EM Reveals Integrin-Mediated TGF-? Activation without Release from Latent TGF-?.

Project description:Integrin ?v?8 binds with exquisite specificity to latent transforming growth factor-? (L-TGF-?). This binding is essential for activating L-TGF-? presented by a variety of cell types. Inhibiting ?v?8-mediated TGF-? activation blocks immunosuppressive regulatory T cell differentiation, which is a potential therapeutic strategy in cancer. Using cryo-electron microscopy, structure-guided mutagenesis, and cell-based assays, we reveal the binding interactions between the entire ?v?8 ectodomain and its intact natural ligand, L-TGF-?, as well as two different inhibitory antibody fragments to understand the structural underpinnings of ?v?8 binding specificity and TGF-? activation. Our studies reveal a mechanism of TGF-? activation where mature TGF-? signals within the confines of L-TGF-? and the release and diffusion of TGF-? are not required. The structural details of this mechanism provide a rational basis for therapeutic strategies to inhibit ?v?8-mediated L-TGF-? activation.

| S-EPMC7238552 | biostudies-literature

Structural determinants of integrin β-subunit specificity for latent TGF-β.

Project description:Eight integrin α-β heterodimers recognize ligands with an Arg-Gly-Asp (RGD) motif. However, the structural mechanism by which integrins differentiate among extracellular proteins with RGD motifs is not understood. Here, crystal structures, mutations and peptide-affinity measurements show that αVβ6 binds with high affinity to a RGDLXXL/I motif within the prodomains of TGF-β1 and TGF-β3. The LXXL/I motif forms an amphipathic α-helix that binds in a hydrophobic pocket in the β6 subunit. Elucidation of the basis for ligand binding specificity by the integrin β subunit reveals contributions by three different βI-domain loops, which we designate specificity-determining loops (SDLs) 1, 2 and 3. Variation in a pair of single key residues in SDL1 and SDL3 correlates with the variation of the entire β subunit in integrin evolution, thus suggesting a paradigmatic role in overall β-subunit function.

| S-EPMC4717663 | biostudies-literature

Preferred orientations of His64 in human carbonic anhydrase II.

Project description:Histidine at position 64 (His64) in human carbonic anhydrase II (HCA II) is believed to be the proton acceptor in the hydration direction and the proton donor in the dehydration direction for the rate-limiting proton transfer (PT) event. Although the biochemical effect of histidine at position 64 has been thoroughly investigated, the role of its orientation in the PT event is a topic of considerable debate. X-ray data of HCA II suggests that His64 can adopt either an "in" or "out" orientation. The "in" orientation is believed to be favored for the hydration direction PT event because the Ndelta of His64 is closer to the catalytic zinc. This orientation allows for smaller water bridges, which are postulated to be more conducive to PT. In the present work, classical molecular dynamics simulations have been conducted to elucidate the role that the His64 orientation may play in its ability to act as a proton donor/acceptor in HCA II. The free energy profile for the orientation of His64 suggests that the histidine will adopt an "in" orientation in the hydration direction, which brings Ndelta in close proximity to the catalytic zinc. When the histidine becomes protonated, it then rotates to an "out" orientation, creating a more favorable solvation environment for the protonated His64. In this "out" orientation, the imidazole ring releases the delta nitrogen's excess proton into the bulk environment. After the second PT event and when the zinc-bound water is regenerated, the His64 is again favored to reorient to the "in" orientation, completing the catalytic cycle.

| S-EPMC2569863 | biostudies-literature

Routine single particle CryoEM sample and grid characterization by tomography.

Project description:Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.

| S-EPMC5999397 | biostudies-literature

Integrin beta6 mediates phospholipid and collectin homeostasis by activation of latent TGF-beta1.

Project description:Surfactant lines the alveolar surface and prevents alveolar collapse. Derangements of surfactant cause respiratory failure and interstitial lung diseases. The collectins, surfactant proteins A and D, are also important in innate host defense. However, surfactant regulation in the postnatal lung is poorly understood. We found that the epithelial integrin, alphavbeta6, regulates surfactant homeostasis in vivo by activating latent transforming growth factor (TGF)-beta. Adult mice lacking the beta-subunit of alphavbeta6 (Itgb6-/-) developed increased bronchoalveolar lavage phospholipids and surfactant proteins A and D, and demonstrated abnormal-appearing alveolar macrophages, reminiscent of the human disease pulmonary alveolar proteinosis. Using lung-specific expression of constitutively active TGF-beta1 in Itgb6-/- mice, we found that TGF-beta1 was sufficient to normalize these abnormalities. Tgfbeta1-deficient mice also demonstrated increased phospholipids and surfactant proteins A and D, but mice lacking the key TGF-beta signaling molecule, SMAD3, did not. Therefore, integrin-mediated activation of latent TGF-beta1 regulates surfactant constituents independent of intracellular SMAD3. In vivo increases in surfactant protein A and D were not associated with increases in mRNA for these proteins in alveolar tissue from Itgb6-/- mice. On the other hand, isolated alveolar macrophages from Itgb6-/- mice were defective in processing phospholipids in vitro, suggesting that reduced surfactant clearance contributes to altered surfactant homeostasis in these mice in vivo. These findings show that alphavbeta6 and TGF-beta1 regulate homeostasis of phospholipids and collectins in adult mouse lungs and may have implications for anti-fibrotic therapeutics that inhibit active TGF-beta in the lung.

| S-EPMC2219547 | biostudies-literature

Epoxidized graphene grid for highly efficient high-resolution cryoEM structural analysis.

Project description:Functionalization of graphene is one of the most important fundamental technologies in a wide variety of fields including industry and biochemistry. We have successfully achieved a novel oxidative modification of graphene using photoactivated ClO2· as a mild oxidant and confirmed the oxidized graphene grid is storable with its functionality for at least three months under N2 atmosphere. Subsequent chemical functionalization enabled us to develop an epoxidized graphene grid (EG-grid™), which effectively adsorbs protein particles for electron cryomicroscopy (cryoEM) image analysis. The EG-grid dramatically improved the particle density and orientation distribution. The density maps of GroEL and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were reconstructed at 1.99 and 2.16 Å resolution from only 504 and 241 micrographs, respectively. A sample solution of 0.1 mg ml-1 was sufficient to reconstruct a 3.10 Å resolution map of SARS-CoV-2 spike protein from 1163 micrographs. The map resolutions of β-galactosidase and apoferritin easily reached 1.81 Å and 1.29 Å resolution, respectively, indicating its atomic-resolution imaging capability. Thus, the EG-grid will be an extremely powerful tool for highly efficient high-resolution cryoEM structural analysis of biological macromolecules.

| S-EPMC9908306 | biostudies-literature

Preferred orientations of garnet porphyroblasts reveal previously cryptic templating during nucleation.

Project description:Electron back scattered diffraction data of garnet crystals from the Nelson Aureole, British Columbia and the Mosher's Island formation, Nova Scotia, reveals that 22 garnet crystals are all oriented with one of three crystal directions parallel to the trace of the foliation plane in thin section. Structural models suggest that these relationships are due to preferential garnet nucleation onto muscovite, with the alignment of repeating rows of Al octahedra and Si tetrahedra in each leading to inheritance of garnet orientation from the muscovite. These results highlight that epitaxial nucleation may be a prevalent process by which porphyroblast minerals nucleate during metamorphism and carry implications for the role that non-classic nucleation pathways play in the crystallization of metamorphic minerals, the distribution of porphyroblasts in metamorphic rocks, and, in cases in which nucleation is the rate limiting step for crystallization, the energetics of metamorphic reactions.

| S-EPMC7994400 | biostudies-literature

Release of active TGF-?1 from the latent TGF-?1/GARP complex on T regulatory cells is mediated by integrin ?8.

Project description:Activated T regulatory cells (Tregs) express latent TGF-?1 on their cell surface bound to GARP. Although integrins have been implicated in mediating the release of active TGF-?1 from the complex of latent TGF-?1 and latent TGF-?1 binding protein, their role in processing latent TGF-?1 from the latent TGF-?1/GARP complex is unclear. Mouse CD4(+)Foxp3(+) Treg, but not CD4(+)Foxp3(-) T cells, expressed integrin ?8 (Itgb8) as detected by quantitative RT-PCR. Itgb8 expression was a marker of thymically derived (t)Treg, because it could not be detected on Foxp3(+)Helios(-) Tregs or on Foxp3(+) T cells induced in vitro. Tregs from Itgb8 conditional knockouts exhibited normal suppressor function in vitro and in vivo in a model of colitis but failed to provide TGF-?1 to drive Th17 or induced Treg differentiation in vitro. In addition, Itgb8 knockout Tregs expressed higher levels of latent TGF-?1 on their cell surface consistent with defective processing. Thus, integrin ?v?8 is a marker of tTregs and functions in a cell intrinsic manner in mediating the processing of latent TGF-?1 from the latent TGF-?1/GARP complex on the surface of tTregs.

| S-EPMC4157079 | 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