A direct-imaging cryo-EM study of shedding extracellular vesicles from leukemic monocytes
Keywords: Cryo-EM; Cell stimulation; Endotoxins; Microparticles; Blebbing; NTA;
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Crystal Structure of the Maturation Protein from Bacteriophage Qβ
Keywords: ssRNA; single-stranded RNA; MBP; maltose-binding protein; cryo-EM; cryo-electron microscopy; SeMet; selenomethionine; RNA phages; QÃ; virus structure; maturation protein;
Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200Â kV
Keywords: cryo-EM; cryo-electron microscopy; DED; direct electron detection; CCD; charge-coupled device; EM; electron microscopy; TEM; transmission electron microscope; dsRNA; double-stranded RNA; RdRp; RNA-dependent RNA polymerase; DQE; detective quantum efficienc
Focus: The interface between data collection and data processing in cryo-EM
Keywords: cryo-EM; Cryo-electron microscopy; DED; Direct electron detector; 2D; Two dimensional; 3D; Three dimensional; CTF; Contrast transfer function; FFT; Fast Fourier transform; GPU; Graphical processing unit; CPU; Central processing unit; MRC; MRC file format;
Real-time detection and single-pass minimization of TEM objective lens astigmatism
Keywords: Astigmatism correction; Objective lens stigmators; Real-time feedback; “Radar”-style display; Single-pass tuning strategy; cryo-EM;
Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions
Keywords: cryo-EM; Cryo Electron Microscope; PTC; peptidyl transferase center; MD; Molecular Dynamics; SMD; Steered Molecular Dynamics; COM; Center-of-Mass; WHAM; Weighted Histogram Analysis Method; ITC; Isothermal Titration Calorimetry; PMF; Potential of Mean Forc
Cryo-EM analysis of a domain antibody bound rotary ATPase complex
Keywords: ATPase; Membrane protein; Cryo-EM; Antibodies;
A Glimpse of Membrane Transport through Structures-Advances in the Structural Biology of the GLUT Glucose Transporters
Keywords: membrane transport; major facilitator superfamily; alternating access; GLUT1; SLC2A; MP; membrane protein; PDB; Protein Data Bank; cryo-EM; electron cryomicroscopy; MFS; major facilitator superfamily; SLC; solute carrier; TM; transmembrane; SP; sugar port
Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations
Keywords: 2D/3D; two dimensional/three dimensional; apoA-I; apolipoprotein A-I; ABC; ATP-binding cassette; CCD; charge-coupled device; DMPC; dimyristoyl phosphatidylcholine; EPR; electron paramagnetic resonance; FPLC; fast protein liquid chromatography; FRET; fluor
Specific interaction of IM30/Vipp1 with cyanobacterial and chloroplast membranes results in membrane remodeling and eventually in membrane fusion
Keywords: A. thaliana; Arabidopsis thaliana; acetyl-CoA; acetyl coenzyme A; ATP; adenosinetriphosphate; C. reinhardtii; Chlamydomonas reinhardtii; CD; circular dichroism; CM; cytoplasmic membrane; cryo-EM; cryo-electron microscopy; CTM; chloroplast translation memb
Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome
Keywords: Bacteriophage; ΦM5; phiM5; T = 7 capsid geometry; Cryo-EM; Rhizophage tail fiber; Sinorhizobium meliloti; Alphaproteobacteria; Icosahedral; Short direct terminal repeat; Terminase; LUZ24 phage; Genome; Proteome; ΦM12; ΦM9; Podovirus;
Methods to account for movement and flexibility in cryo-EM data processing
Keywords: Cryo-EM; RELION; Image processing; Motion correction;
Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism
Keywords: 2D; two-dimensional; 3D; three-dimensional; cryo-EM; cryo-electron microscopy; CTF; contrast transfer function; FSC; Fourier Shell Correlation; MST; 3-mercaptopyruvate:sulfur transferase; MTF; modulation transfer function; SQR; sulfide quinone reductase;
The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region
Keywords: TREX-2; transcription-export complex-2; mRNA nuclear export; TREX-2 complex; Cryo-EM; Crystallography;
DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM
Keywords: Cryo-EM; Particle picking; Automation; Deep learning;
Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens
Keywords: Electron cryomicroscopy; Single-particle reconstruction; Electron tomography; Gold supports; Cryo-EM; Protein structure;
Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting
Keywords: Cryo-EM; Protein-protein interface; Evolutionary conservation; Cryo-EM density based fitting and modeling;
Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages
Keywords: ssRNA; single-stranded RNA; VLP; virus-like particle; MAS; magic-angle spinning; 3D; three-dimensional; SeMet; selenomethionine Tobacco Etch Virus, TEV; cryo-EM; cryo-electron microscopy; RNA bacteriophage; Leviviridae; coat protein; virus-like particle;
Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage
Keywords: Cryo-EM; Automation; Dose fractionation;
Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring
Keywords: VCP; ATPase; VCP cofactors interaction; Cryo-EM; Mutations and disease;
Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images
Keywords: Cryo-EM; Direct electron detector; Direct detector device; Anisotropic magnification; Distortion; Correction; Contrast transfer function; Differential magnification;
Visualization of adherent cell monolayers by cryo-electron microscopy: A snapshot of endothelial adherens junctions
Keywords: Cryo-EM; CEMOVIS; Adherens junction; VE-cadherin;
Alignment of cryo-EM movies of individual particles by optimization of image translations
Keywords: Cryo-EM; Beam-induce motion; Direct detector device; DDD; Local drift; Motion correction; Algorithm; Direct electron detector; Movie;
FEI's direct electron detector developments: Embarking on a revolution in cryo-TEM
Keywords: DQE; MTF; CMOS; Electron counting; Direct electron detector; Cryo-EM; TEM;
The Cryo-EM structure of the CorA channel from Methanocaldococcus jannaschii in low magnesium conditions
Keywords: TmCorA; Thermotoga maritima CorA; MjCorA; Methanocaldococcus jannaschii; ATP; adenosine tri-phosphate; TM; trans-membrane; RMS; root mean square; DDM; dodecylmaltoside; SAXS; Small Angle X-ray Scattering; Cryo-EM; Cryo-Electron Microscopy; FSC; Fourier Sh
Nature׳s favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold
Keywords: cryo-EM; electron cryomicroscopy; 3D; three-dimensional; T; triangulation; gp; gene product; su; suppressor; tsf; temperature-sensitive-folding; am; amber mutation; WT; wild-type; HK97-fold; Capsid protein structure; Bacteriophage; Coat protein; Accessory
Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct
Keywords: Exos; exosomes; sMVs; shed microvesicles; EVs; extracellular vesicles; CM; culture medium; CCM; concentrated culture medium; PDCD6IP/Alix; programmed cell death 6 interacting protein; TSG101; tumour susceptibility 101; ESCRT; endosomal sorting complex req
Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications
Keywords: Bolaamphiphiles; Molecular dynamics simulations; Cryo-EM; FRET; siRNA drug delivery; RNAi induced gene silencing;
The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis
Keywords: DNA-dependent protein kinase; Non-homologous end joining; Mitosis; ATM; ataxia telangiectasia mutated; ATR; ATM- and Rad3-related; ds; double-stranded; cryo-EM; cryo-electron microscopy; DSB; DNA double strand break; DNA-PK; DNA-activated/dependent protei
Technical Note2dx_automator: Implementation of a semiautomatic high-throughput high-resolution cryo-electron crystallography pipeline
Keywords: 2D; two dimensions/dimensional; 3D; three dimensions/dimensional; CCD; charge coupled devices; CMOS; complementary metal-oxide-semiconductor; cryo-EM; cryo-electron microscopy; CTF; contrast transfer function; DED; direct electron detector; EM; electron m
Fabrication of carbon films with â¼500Â nm holes for cryo-EM with a direct detector device
Keywords: cryo-EM; Holey carbon; Specimen preparation; Direct detector; Contrast transfer function; Nanofabrication;
Single particle 3D reconstruction for 2D crystal images of membrane proteins
Keywords: Cryo-electron crystallography; Membrane proteins; Single-particle analysis; High performance computing; GPGPU; 2dx; 2D; two dimensions/dimensional; 3D; three dimensions/dimensional; CM; center of mass; CNDBs; cyclic nucleotide binding domains; cryo-EM; cr
Frealix: Model-based refinement of helical filament structures from electron micrographs
Keywords: WLC; worm-like chain; Aβ; amyloid beta; Amyloid; Structure; Cryo-EM; Curvature; Filament; Helical;
The mechanism of negative DNA supercoiling: A cascade of DNA-induced conformational changes prepares gyrase for strand passage
Keywords: ADPNP; 5â²-adenosine-β,γ-imidotriphosphate; CTD; C-terminal domain (of GyrA); cryo-EM; cryo-electron microscopy; FRET; fluorescence resonance energy transfer; G-segment; gate segment; GHKL; GyrB-Hsp90-histidine/serine protein kinases-MutL; NTD; N-termi
Reprint of “The mechanism of negative DNA supercoiling: A cascade of DNA-induced conformational changes prepares gyrase for strand passage”
Keywords: ADPNP; 5â²-adenosine-β,γ-imidotriphosphate; CTD; C-terminal domain (of GyrA); cryo-EM; cryo-electron microscopy; FRET; fluorescence resonance energy transfer; G-segment; gate segment; GHKL; GyrB-Hsp90-histidine/serine protein kinases-MutL; NTD; N-termi
Rotationally invariant image representation for viewing direction classification in cryo-EM
Keywords: Cryo-EM; 2D classification; Single particle reconstruction;
Methods for testing Zernike phase plates and a report on silicon-based phase plates with reduced charging and improved ageing characteristics
Keywords: Phase plate; Zernike; CTF; Image contrast; Cryo-EM; Cryo-tomography;
Minimizing electrostatic charging of an aperture used to produce in-focus phase contrast in the TEM
Keywords: Phase contrast; Charging; Cryo-EM; Phase plate;
Hybrid electron microscopy-FRET imaging localizes the dynamical C-terminus of Tfg2 in RNA polymerase II-TFIIF with nanometer precision
Keywords: Nano-probe; Cryo-EM; Transcription; Malleable protein; Bio-conjugation;
Affinity grid-based cryo-EM of PKC binding to RACK1 on the ribosome
Keywords: Affinity grid; Cryo-EM; RACK1; PKC βII; Ribosome
Cryo-electron tomography of bacterial viruses
Keywords: Bacteriophage; Cryo-electron microscopy; Cryo-EM; Cryo-electron tomography; Cryo-ET; Sub-tomogram averaging
TMaCS: A hybrid template matching and classification system for partially-automated particle selection
Keywords: Cryo-EM; Software; Particle picking; Particle selection; Automated; Machine learning; Template matching; Single particle
Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies
Keywords: Electron microscopy; Cryo-EM; Bayesian inference; Ensemble refinement; Validation; Disorder; GroEL; ESCRT
Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals
Keywords: Cryo-EM; Specimen preparation; Biotinylation; Streptavidin;
A site-specific focused-ion-beam lift-out method for cryo Transmission Electron Microscopy
Keywords: Cryo-SEM; Cryo-FIB; Cryo-TEM; Specimen thinning; Frozen-hydrated sample; Cryo-EM; FIB; TEM; Sample preparation;
Computational methods for prediction of protein-RNA interactions
Keywords: AUC; area under receiver operating characteristic curve; cryo-EM; cryo-electron microscopy; DARS-RNP; decoys as reference state based potential to assess structure of protein-RNA complexes; FPR; false positive rate (1 - specificity); HMM; Hidden Marko
Comparative structural analysis of eukaryotic flagella and cilia from Chlamydomonas, Tetrahymena, and sea urchins
Keywords: Flagella; Cilia; Axoneme; Dynein; Electron tomography; Cryo-EM;
SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles
Keywords: Single-particle; Software; Ab initio reconstruction; Flexibility; Cryo-EM; Heterogeneity; Alignment; Open source; Refinement; Clustering; Image processing; Common lines; Fourier analysis;
A graph theory method for determination of cryo-EM image focuses
Keywords: Cryo-EM; Contrast transfer function; Defocus; Linear least square; Graph theory