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11 results for “CryoEM”
CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge
<p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map Challenge hosted at challenges.emdatabank.org are deposited.</p> <p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p> <p>Seven benchmark raw image datasets were selected for the challenge. Six are selected from recently described single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. All of the raw image datasets are archived at pdbe.org/empiar.</p> <p>27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details. 15 of the reconstructions were calculated using the SDSC Gordon supercomputer.</p> <p>This map challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.</p> <p> </p>
CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge
<p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Models Challenge hosted at challenges.emdatabank.org are deposited.</p> <p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p> <p>Eight recently determined target structures were selected for the challenge. All of the maps were archived in the EM Data Bank (EMDB; http://emdatabank.org).</p> <p>In total 16 Challengers created 106 models and uploaded their results with associated details. In the zip files, each entry is represented in a folder containing the original deposition upload (deposited_EM.pdb), initial processing at RCSB/Rutgers (deposited_EM_edited.pdb, maxit.cif, maxit.cif.pdb) and final model version evaluated (model-compare.pdb) at UC Davis (http://model-compare.emdatabank.org).</p> <p>This model challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.</p> <p> </p>
Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
<p>These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 & Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs.</p> <p>For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script <em>calc-density.tcl</em>. </p> <p><strong>In VMD TK-Console:</strong></p> <p>> mol new <system>.psf<br> > mol addfile <system>.dcd waitfor all<br> > source /path/to/scripts/LipNetwork.tcl<br> > align<br> > source /path/to/scripts/calc-density.tcl<br> > dmpcdensity <outname><br> [output] outname_ltailden.dx<br> <br> Convert from .dx to .mrc using <em>UCSF-Chimera Volume_Viewer</em> plugin.<br> [output] outname_ltailden.mrc<br> <br> <strong>Using Relion:</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [output] outname_ltailden_D6-Sym.mrc</p> <p> </p> <p>All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame).</p> <p>For questions regarding MD-data analysis and full trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).</p>
High resolution cryoEM structure of huntingtin in complex with HAP40
<p><strong>High resolution cryoEM structure of huntingtin in complex with HAP40</strong></p> <p>This dataset relates the following depositions in the PDB: 6X9O and EMDB: EMD-22106 which are the structure solution of HTT-HAP40 complex at 2.6 angstrom resolution by cryoEM. </p> <p>Files contained within this dataset are detailed in the "Upload_information.xlsx" file. </p> <p> </p>
Preparation of dephosphorylated HTT samples for cryoEM analysis 2019/03/20
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Preparation of dephosphorylated HTT samples for cryoEM analysis</p> <p><strong>Date completed:­ </strong>2019/03/20</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p>
Analysis of dephosphorylated HTT samples for cryoEM analysis and further sample preparation 2019/04/15
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Analysis of dephosphorylated HTT samples for cryoEM analysis and further sample preparation</p> <p><strong>Date completed:­ </strong>2019/04/15</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p>
Analysis of dephosphorylated HTT samples by cryoEM analysis 2019/05/01
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Analysis of dephosphorylated HTT samples by cryoEM analysis </p> <p><strong>Date completed:­ </strong>2019/05/01</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p> <p> </p>
Huntingtin-RNA complex generation for cryoEM analysis 2019/07/24
<p><strong>Project: </strong>High resolution structural analysis of HTT-nucleic acid complexes</p> <p><strong>Experiment: </strong>Huntingtin-RNA complex generation for cryoEM analysis</p> <p><strong>Date: </strong>2019/07/24</p> <p><strong>Background: </strong>Huntingtin has been shown to copurify with nucleic acid material as well as bind different nucleic acid species in band shift assays. To more thoroughly characterise this interaction, HTT-nucleic acid complex generation and structure solution should provide insight into how huntingtin performs this function. </p> <p><strong>Rationale: </strong>Previous attempts to capture HTT-nucleic complexes have been difficult and maintaining the complex throughout purification of the sample has been tricky. These four approaches are different ways to try and form a stable complex between Q54 HTT-HAP40 and CAG<sub>8</sub>RNA. </p>
HARP Analysis of cryoEM Structures in the PDB
<p><i>HARP_results.hdf5</i> contains the results of a hierarchical atomic resolution perception (HARP) calculation on each of the cryoEM structures deposited in the Protein Data Bank (PDB) prior to January 1, 2023. Top-level group names are the PDB IDs of the structures. HDF5 group attributes for each entry are certain metadata extracted from the mmCIF files associated with each entry. HDF5 datasets within each group are indexed relative to each other (<i>i.e.</i>, are of the same length). They are:</p><ul><li>authids (char): the author deposited ID of each residue (<i>e.g.</i>, "114")</li><li>chains (char): the chain ID of each residue (<i>e.g.</i>, "AC")</li><li>resids (int): the residue index of each residue (<i>e.g.</i>, 12)</li><li>renames (char): the residue name of each residue (<i>e.g.</i>, "cys")</li><li>probs (double): the HARP probability value, P, for each residue (<i>e.g.</i>, 0.897)</li></ul>
Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering
<p>MD trajectories for use with the analysis code in https://github.com/bylehn/ifnl4-structure-paper</p>
Identification of human tRNA molecules bound to human cytomegalovirus capsid using cryoEM and Next-generation sequencing
GEO Series GSE167037. Homo sapiens. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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