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38 results for “Membrane Structures”
Homologous membrane protein structures (HOMEP) version 1
<p><strong>Table 1</strong> = List of membrane protein structures in the <strong>HOMEP</strong> data set (version 1).<br> From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 1)<br> <a href="https://www.ncbi.nlm.nih.gov/pubmed/16648166">https://www.ncbi.nlm.nih.gov/pubmed/16648166</a></p> <p>Contains the following columns:<br> PDB-Code Protein-Name Source Res-(Å) Length (Num-TM) Number-of-TM-domains Family</p> <p><strong>Table 2</strong> = List of pairs of membrane protein structures in the <strong>HOMEP</strong> data set (version 1).<br> From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 2)</p> <p>Contains the following columns:<br> Model Family Query Template ID(%) RMS(Å) GDT_TS(%) TM-ID(%) TM-RMS(Å) TM GDT_TS(%)</p> <p><strong>Table 3 </strong>= Manually-defined transmembrane regions in the <strong>HOMEP</strong> data set (version 1), listed for each family by transmembrane segment number. From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 3).</p> <p>Contains the columns defined as follows:<br> Protein chain identifier, start (-s) and end (-e) residues for each PDB structure in the family</p>
Homologous membrane protein structures (HOMEP) dataset version v2
<p><strong>Protein structures from the dataset of Homologous MEmbrane Protein structures (HOMEP)</strong> version v2 created in 2010, published in 2013. A more automated version of HOMEP v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a><br> </p> <p><strong>Table 1</strong> = List of protein databank structure entries<br> From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 1, with the following entries:<br> Family grouping, Protein databank identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>Table 2</strong> = List of pairs of structures<br> From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 2, with the following entries:<br> Family grouping, PDB code for first structure, Chain ID from PDB1, PDB for second structure, Chain ID from PDB2, protein structural difference (PSD), % sequence identity</p> <p> </p> <p><strong>File S2 HOMEP2 Dataset.tar.gz</strong> = Protein databank format files (PDB) are attached in the Dataset tar zipped file, organized by family. From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary dataset.</p>
Tabular datasets for "In situ structural analysis reveals membrane shape transitions during autophagosome formation"
<p>Tabular source data for all plots in the manuscript "In situ structural analysis reveals membrane shape transitions during autophagosome formation". The article is available at https://doi.org/10.1101/2022.05.02.490291. The naming of the sheets in the .xlsx files corresponds to the figure number and panel.</p>
X-Ray Diffraction data from Membrane transport protein AcrB, V612F mutant with bound minocycline, source of 9FHC structure
<p>Crystals were grown of the membrane transport protein AcrB, V612F mutant, with bound minocycline. </p> <p>X-ray diffraction data of this upload: 400 frames of 0.5° width were collected on 2007-04-30 at the X06SA beamline of Swiss Light Source at Paul-Scherrer-Institute (Switzerland).</p> <p>The data can be processed with XDS; XDS.INP is provided as part of the upload.</p> <p>The data are the basis of the PDB 9FHC structure.</p>
Homologous membrane protein structures (HOMEP) version 3
<p><strong>Homologous membrane protein structures (HOMEP)</strong> version 3 (created 2013)<br> An updated version of v2 <a href="https://doi.org/10.5281/zenodo.2646539">10.5281/zenodo.2646539</a> and v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a></p> <p><strong>Table 1</strong> = Alpha-helical membrane protein structures in the HOMEP3 data set (2013), listed by family<br> From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 1):<a href="http://https://www.ncbi.nlm.nih.gov/pubmed/26178143"> https://www.ncbi.nlm.nih.gov/pubmed/26178143</a> </p> <p>Contains the following columns:<br> Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>Table 2</strong> = Beta-barrel membrane protein structures in the HOMEP3 data set (2013), listed by family<br> From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 2)</p> <p>Contains the following columns:<br> Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>HOMEP3_pairs_alpha.txt</strong><br> List of all pairs of protein structure chains of alpha-helical proteins</p> <p> </p> <p><strong>HOMEP3_pairs_beta.txt</strong><br> List of all pairs of protein structure chains of beta-barrel proteins</p> <p> </p> <p><strong>HOMEP3_pdbs.tar.gz</strong><br> All pdb files for individual chains in both alpha-helical and beta-barrel subsets</p>
Simulation data and code used for the publication in Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes"
<p>Simulation data used in the publication Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes". The simulation data set, and the code developed to generate such data, are included. Details in the published paper </p>
Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat
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PART-2: Dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>Complementary file for the attached files<br> Written 24-04-2017<br> by Robert Bleischwitz (modellwerft@freenet.de)</p> <p>General Comments</p> <p>0.) This specific upload contains PART-2 of the full dataset</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload contains PART-2 of the full dataset, including introduction file + membrane-wing case (Load+DIC+PIV measurements) </p>
PART-1: Dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>Complementary file for the attached files<br> Written 24-04-2017<br> by Robert Bleischwitz (modellwerft@freenet.de)</p> <p>General Comments</p> <p>0.) This specific upload contains PART-1 of the full dataset</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload contains PART-1 of the full dataset, including introduction file + rigid flat-plate case (Load+PIV measurements) as reference to membrane wing case (PART-2)</p>
Full dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>0.) Version: 18.May 2017</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload is zipped and contains all necessary files to reconstruct the time-resolved dataset.</p>
Coordinate files from LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
<p>Coordinate files from the first and last frame of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations used throughout the LipIDens pipeline.</p><p>CG simulations were run for HHAT, OTOP1, ELIC, MscS, TRPV6, ChRmine, Ste2, Connexin-50, NPC1 and the PAT complex. All CG simulations were run for 10 x 15 μs with the exception of NPC1 which was simulated for 10 x 30 μs.</p><p>AT simulations were run for HHAT (5 x 200 ns) and ELIC (3 x 200 ns) in apo configurations.</p><p><strong>File description:</strong></p><p>Directories for each protein are listed with the suffix CG or AT used to indicate the simulation resolution. </p><p>md_fit_firstframe_<i>X</i>.gro - GROMACS structure file for the first frame of replicate <i>X</i>. </p><p>md_fit_lastframe_<i>X</i>.gro - GROMACS structure file for the last frame of replicate <i>X</i>. </p>
Presentation in 45th ARO: Multiphoton imaging for 3-D morphometry and characterization of fiber structure of the full human tympanic membrane
<p>This is a poster presentation in t<span>he 45th Association for Research in Otolaryngology Mid-Winter Meeting 2022, and the image files used for the poster.</span></p>
Presentation in HEARING: High-resolution structural and functional EAR imaging 2023: Three-dimensional vibration of the human tympanic membrane using a scanning laser doppler vibrometer
<p>This is for Bastian Baselt's poster presentation in HEARING: High-resolution structural and functional EAR imaging, Ascona, Switzerland in 2023, and the related data.</p>
Conserved structural elements specialize ATAD1 as a membrane protein extraction machine
<p>The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria's protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1's mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. Among these features in Msp1 was the utilization of multiple aromatic amino acids to firmly grip the substrate in the central pore. However, it was not clear whether the aromatic nature of these amino acids were required, or if they could be functionally replaced by aliphatic amino acids. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. We developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1's activity in live cells and showed that both aromatic amino acids in pore-loop 1 are required for ATAD1's function and cannot be substituted by aliphatic amino acids. A short α-helix at the C-terminus strongly facilitates ATAD1's oligomerization, a structural feature that distinguishes ATAD1 from its closely related proteins.</p>
Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy Raw GUV Data
<p>Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.</p>
Subset of non-redundant, high resolution multi-pass membrane protein PDB structure files from OPM
<p>A subset of OPM PDB structure files with membrane predictions curated for the MSc thesis project '<strong>Structural characterization of triplets of transmembrane α-helical segments consecutive in sequence in integral membrane proteins: a fragment-based computational pipeline'. </strong>The dataset contains PDB files downloaded from OPM on 22/02/2023. The files are alpha-helical integral membrane proteins with at least three transmembrane regions at better than 2.7 Angtrom resolution. They are non-redundant, with a sequence identity of less than 40% based on clustering with the cd-hit algorithm. </p>
Source Data: Structure and inhibition of SARS-CoV-2 spike refolding in membranes
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Conserved structural elements specialize ATAD1 as a membrane protein extraction machine
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Figs. 5–8 in A Method to Observe Membranous Structures of Female Genitalia in the Inflated Condition (Coleoptera: Cerambycidae)
Figs. 5–8. Comparison of female genital organs in natural and artificial conditions. 5) Oberea sobosana, deflated natural condition, lateral view; 6) O. sobosana, artificially inflated condition, lateral view; 7) Hypocacia fruhstorferi, inflated naturally, lateral view; 8) H. fruhstorferi, artificially inflated condition, lateral view. Scale = 1 mm. Comparisons are made between conditions of the same specimen. The slight differences between Figs. 7–8 are due to the inner pressure of inflation. The genitalia are fully inflated in the artificial condition, but have slightly lower pressure in the natural condition.
Figs. 1–4. The method for inflating the female genital organ. 1 in A Method to Observe Membranous Structures of Female Genitalia in the Inflated Condition (Coleoptera: Cerambycidae)
Figs. 1–4. The method for inflating the female genital organ. 1) Insert nozzle or needle from gonopore to near the distal part of the vagina or bursa copulatrix; 2) Inject petroleum jelly to inflate membranous parts; 3) Clamp median oviduct when jelly flows from oviduct cavity; 4) Carefully extract nozzle from gonopore after inflation.
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