Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single particle cryo-EM dataset of clathrin cages suitable for subparticle extraction

ABSTRACT:

SUBMITTER: Corinne J Smith

PROVIDER: EMPIAR-10295 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly.

Morris Kyle L KL Jones Joseph R JR Halebian Mary M Wu Shenping S Baker Michael M Armache Jean-Paul JP Avila Ibarra Amaurys A Sessions Richard B RB Cameron Alexander D AD Cheng Yifan Y Smith Corinne J CJ

Nature structural & molecular biology 20191003 10

Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. We present the cryo-EM structure and molecular model of assembled porcine clathrin, providing insights into interactions that stabilize key elements of the clathrin lattice, namely, between adjacent heavy chains, at the light chain-heavy chain interface and within the trimerization domain. Furthermor ...[more]

PMID: 31582853

Similar Datasets

Single particle cryo-EM dataset of clathrin cages with phase flipping suitable for refinement

Project description: Not available

| EMPIAR-10294 | biostudies-other

Single particle cryo-EM dataset of the triskelion hub subparticle extraction from clathrin cages

Project description: Not available

| EMPIAR-10296 | biostudies-other

Single particle cryo-EM dataset for LetB from E.coli

Project description: Not available

| EMPIAR-10350 | biostudies-other

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 dataset of human adenovirus HAdV-D26

Project description: Not available

| EMPIAR-10455 | biostudies-other

Single-particle cryo-EM dataset of the Vairimorpha necatrix ribosome

Project description: Not available

| EMPIAR-11075 | biostudies-other

Single particle cryo-EM dataset of Mus musculus mitochondrial complex I

Project description: Not available

| EMPIAR-11527 | biostudies-other

Single particle cryo-EM dataset of Yarrowia lipolytica mitochondrial complex I

Project description: Not available

| EMPIAR-11662 | 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

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