Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-particle Cryo-EM of the endogenous human BAF complex alone

ABSTRACT:

SUBMITTER: Thomas Walz

PROVIDER: EMPIAR-10590 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms.

Mashtalir Nazar N Suzuki Hiroshi H Farrell Daniel P DP Sankar Akshay A Luo Jie J Filipovski Martin M D'Avino Andrew R AR St Pierre Roodolph R Valencia Alfredo M AM Onikubo Takashi T Roeder Robert G RG Han Yan Y He Yuan Y Ranish Jeffrey A JA DiMaio Frank F Walz Thomas T Kadoch Cigall C

Cell 20201013 3

Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture. Here, we present a structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy (cryo-EM), cross-linking mass spectrometry, and homology modeling. BAF complexes bilaterally engage the nucleosome H2A/H2B acidic patch regions through the SMARCB1 C-terminal α-helix and the SMARCA4/2 C-terminal SnAc/post-SnAc re ...[more]

PMID: 33053319

Similar Datasets

Benchmarking cryo-EM Single Particle Analysis Workflow.

Project description:Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase.

| S-EPMC6009202 | biostudies-literature

Single-particle cryo-EM at atomic resolution.

Project description:The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years1,2. However, it has proved difficult to obtain cryo-EM reconstructions with sufficient resolution to visualize individual atoms in proteins. Here we use a new electron source, energy filter and camera to obtain a 1.7 Å resolution cryo-EM reconstruction for a human membrane protein, the β3 GABAA receptor homopentamer3. Such maps allow a detailed understanding of small-molecule coordination, visualization of solvent molecules and alternative conformations for multiple amino acids, and unambiguous building of ordered acidic side chains and glycans. Applied to mouse apoferritin, our strategy led to a 1.22 Å resolution reconstruction that offers a genuine atomic-resolution view of a protein molecule using single-particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualized in difference maps, allowing a direct analysis of hydrogen-bonding networks. Our technological advances, combined with further approaches to accelerate data acquisition and improve sample quality, provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery.

| S-EPMC7611073 | biostudies-literature

Single particle cryo EM Data of a human Akirin2 proteasome complex

Project description: Not available

| EMPIAR-10752 | biostudies-other

Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis.

Project description:The insulin receptor is a dimeric protein that has a crucial role in controlling glucose homeostasis, regulating lipid, protein and carbohydrate metabolism, and modulating brain neurotransmitter levels. Insulin receptor dysfunction has been associated with many diseases, including diabetes, cancer and Alzheimer's disease. The primary sequence of the receptor has been known since the 1980s, and is composed of an extracellular portion (the ectodomain, ECD), a single transmembrane helix and an intracellular tyrosine kinase domain. Binding of insulin to the dimeric ECD triggers auto-phosphorylation of the tyrosine kinase domain and subsequent activation of downstream signalling molecules. Biochemical and mutagenesis data have identified two putative insulin-binding sites, S1 and S2. The structures of insulin bound to an ECD fragment containing S1 and of the apo ectodomain have previously been reported, but details of insulin binding to the full receptor and the signal propagation mechanism are still not understood. Here we report single-particle cryo-electron microscopy reconstructions of the 1:2 (4.3?Å) and 1:1 (7.4?Å) complexes of the insulin receptor ECD dimer with insulin. The symmetrical 4.3?Å structure shows two insulin molecules per dimer, each bound between the leucine-rich subdomain L1 of one monomer and the first fibronectin-like domain (FnIII-1) of the other monomer, and making extensive interactions with the ?-subunit C-terminal helix (?-CT helix). The 7.4?Å structure has only one similarly bound insulin per receptor dimer. The structures confirm the binding interactions at S1 and define the full S2 binding site. These insulin receptor states suggest that recruitment of the ?-CT helix upon binding of the first insulin changes the relative subdomain orientations and triggers downstream signal propagation.

| S-EPMC5886813 | biostudies-literature

LAT1 (SLC7A5) and CD98hc (SLC3A2) complex dynamics revealed by single-particle cryo-EM.

Project description:Solute carriers are a large class of transporters that play key roles in normal and disease physiology. Among the solute carriers, heteromeric amino-acid transporters (HATs) are unique in their quaternary structure. LAT1-CD98hc, a HAT, transports essential amino acids and drugs across the blood-brain barrier and into cancer cells. It is therefore an important target both biologically and therapeutically. During the course of this work, cryo-EM structures of LAT1-CD98hc in the inward-facing conformation and in either the substrate-bound or apo states were reported to 3.3-3.5 Å resolution [Yan et al. (2019), Nature (London), 568, 127-130]. Here, these structures are analyzed together with our lower resolution cryo-EM structure, and multibody 3D auto-refinement against single-particle cryo-EM data was used to characterize the dynamics of the interaction of CD98hc and LAT1. It is shown that the CD98hc ectodomain and the LAT1 extracellular surface share no substantial interface. This allows the CD98hc ectodomain to have a high degree of movement within the extracellular space. The functional implications of these aspects are discussed together with the structure determination.

| S-EPMC7285653 | biostudies-literature

Single Particle Cryo-EM of the PARIS immune complex

Project description: Not available

| EMPIAR-11832 | biostudies-other

Single particle cryo-EM of H. thermophilus chaperonin complex

Project description: Not available

| EMPIAR-11901 | biostudies-other

Single particle cryo-EM of H. thermoluteolus chaperonin complex

Project description: Not available

| EMPIAR-11900 | biostudies-other

Frealign: An Exploratory Tool for Single-Particle Cryo-EM.

Project description:Frealign is a software tool designed to process electron microscope images of single molecules and complexes to obtain reconstructions at the highest possible resolution. It provides a number of refinement parameters and options that allow users to tune their refinement to achieve specific goals, such as masking to classify selected regions within a particle, control over the refinement of specific alignment parameters to accommodate various data collection schemes, refinement of pseudosymmetric particles, and generation of initial maps. This chapter provides a general overview of Frealign functions and a more detailed guide to using Frealign in typical scenarios.

| S-EPMC6760665 | biostudies-literature

Single-particle Cryo-EM of the Thermococcus gammatolerans McrBC complex

Project description: Not available

| EMPIAR-10583 | biostudies-other