Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-particle cryo–negative-stain EM dataset of the compact conformer of kinesin-1 (Kif5C/KLC1)

ABSTRACT:

SUBMITTER: Johannes Weijman

PROVIDER: EMPIAR-11357 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Molecular architecture of the autoinhibited kinesin-1 lambda particle.

Weijman Johannes F JF Yadav Sathish K N SKN Surridge Katherine J KJ Cross Jessica A JA Borucu Ufuk U Mantell Judith J Woolfson Derek N DN Schaffitzel Christiane C Dodding Mark P MP

Science advances 20220916 37

Despite continuing progress in kinesin enzyme mechanochemistry and emerging understanding of the cargo recognition machinery, it is not known how these functions are coupled and controlled by the α-helical coiled coils encoded by a large component of kinesin protein sequences. Here, we combine computational structure prediction with single-particle negative-stain electron microscopy to reveal the coiled-coil architecture of heterotetrameric kinesin-1 in its compact state. An unusual flexion in t ...[more]

PMID: 36112680

Similar Datasets

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

High resolution single particle Cryo-EM refinement using JSPR.

Project description:JSPR is a single particle cryo-EM image processing and 3D reconstruction software developed in the Jiang laboratory at Purdue University. It began as a few refinement scripts for symmetric and asymmetric reconstructions of icosahedral viruses, but has grown into a comprehensive suite of tools for building ab initio reconstructions, high resolution refinements of viruses, protein complexes of arbitrary symmetries including helical tubes/filaments, and image file handling utilities. In this review, we will present examples achieved using JSPR and demonstrate recently implemented features of JSPR such as multi-aberration "alignments" and automatic optimization of masking for the assessment of map resolution using "true" FSC.

| S-EPMC7779749 | biostudies-literature

Single particle cryo-EM dataset for E. coli MlaFEDB bound to MlaC

Project description: Not available

| EMPIAR-11354 | biostudies-other