3d cryo em structure  (Thermo Fisher)

Journal: bioRxiv

Article Title: Structural architecture of amyloid-β oligomers, curvilinear protofibrils and annular assemblies, imaged by cryo-EM and cryo-ET

doi: 10.1101/2024.03.01.582902

Figure Lengend Snippet: Overview of prefibrillar assemblies as a heterogeneous snap-shot, imaged by cryo-EM. Typical classification of assemblies, and approximate number of Aβ 42 monomers is indicated (A). Abinitio 3D reconstruction from 2.5 million particles, 3 structures from 10 are shown. Oligomer (blue) from 180k particles; Curvilinear Protofibril (green) 322k particles and Annular assembly (pink) 298 particles. Scale Bar 20 Å for 2D class averages; 50 Å for 3D structures.

Article Snippet: Importantly, the 3D cryo-EM structure shown in Figure S5 contains an internal channel running through the middle of the structure.

Techniques: Cryo-EM Sample Prep

Journal: bioRxiv

Article Title: Structural architecture of amyloid-β oligomers, curvilinear protofibrils and annular assemblies, imaged by cryo-EM and cryo-ET

doi: 10.1101/2024.03.01.582902

Figure Lengend Snippet: Cryo-EM 2D class averages of typical oligomers and curvilinear protofibrils. 209,000 particles in total, scale bar 20 Å. The class averages have been arranged in increasing length. Top row 25-50 Å, second row 60-80 Å; 3 rd row 90-105 Å; and bottom row 100-140 Å, (A). Distribution of oligomer and curvilinear protofibrils length. Taken from half a million particles; 95 % of particles are less than 90 Å long (B). Density profiles of the protofibril diameter. Six profiles for each row (Red, orange yellow left side images. Green, blue and purple on the right side) (C). Diameters observed for each row. The mean diameter for class averages in rows 2, 3 and 4 are consistently 28 +/-1 Å (standard dev.) (D).

Article Snippet: Importantly, the 3D cryo-EM structure shown in Figure S5 contains an internal channel running through the middle of the structure.

Techniques: Cryo-EM Sample Prep

Journal: bioRxiv

Article Title: Structural architecture of amyloid-β oligomers, curvilinear protofibrils and annular assemblies, imaged by cryo-EM and cryo-ET

doi: 10.1101/2024.03.01.582902

Figure Lengend Snippet: Cryo-ET 3D tomograms. (A) Typical oligomers, side and orthogonal top view are shown (top row), and curvilinear protofibrils (row 2 & 3). The cryo-ET single particles have a close resemblance to the cryo-EM class averages, shown in . Lengths of the long axis are: Top row 25-50 Å; 2 nd row 60-100 Å; 3 rd row 100-300 Å. Images are presented as sums of 5-10 2D slices, each 7.8 Å thick. Scale Bar = 100 Å. (B) Density profiles show that the particles have a consistent diameter of ca . 2.8 nm.

Article Snippet: Importantly, the 3D cryo-EM structure shown in Figure S5 contains an internal channel running through the middle of the structure.

Techniques: Tomography, Cryo-EM Sample Prep

Journal: bioRxiv

Article Title: Structural architecture of amyloid-β oligomers, curvilinear protofibrils and annular assemblies, imaged by cryo-EM and cryo-ET

doi: 10.1101/2024.03.01.582902

Figure Lengend Snippet: Cryo-EM 3D reconstruction of Aβ 42 annular oligomers. 2D averages (A) and 3D reconstruction (B) from 6k single particles suggests the structure has an internal pore. External Diameter, of top view is 65-55 Å; Length of channel is 54 Å; Volume suggests 12-16 Aβ 42 molecules. Scale bar: 50 Å for 3D structures, 20 Å for 2D averages.

Article Snippet: Importantly, the 3D cryo-EM structure shown in Figure S5 contains an internal channel running through the middle of the structure.

Techniques: Cryo-EM Sample Prep

Journal: International Journal of Molecular Sciences

Article Title: Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

doi: 10.3390/ijms20174186

Figure Lengend Snippet: Basic workflow of Cryo-Electron Microscopy (Cryo-EM). Image collected at low dose electron can be analyzed by single-particle or sub-tomogram averaging. However, samples must be vitrified by flash-freezing.

Article Snippet: Volta Phase Plate (VPP), a type of phase plate technology, yielded the first high resolution cryo-EM 3D structures of hemoglobin [ ], G-protein coupled receptor [ ], streptavidin [ ], and the nucleosome [ ].

Techniques: Electron Microscopy, Cryo-EM Sample Prep, Single Particle

Journal: International Journal of Molecular Sciences

Article Title: Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

doi: 10.3390/ijms20174186

Figure Lengend Snippet: Structural characterization of rabbit RyR1 by single-particle cryo-EM (protein data bank (PDB) ID: 5T15) and a set of commonly used predictors of intrinsic disorder. ( A ). Side view of the channel in a space-fill representation. ( B ). Membrane-side view of the channel in a space-fill representation. ( C ). Cytoplasmic-side view of the channel in a space-fill representation. ( D ). Side view of the channel in a cartoon representation. ( E ). Membrane-side view of the channel in a cartoon representation. ( F ). Cytoplasmic-side view of the channel in a cartoon representation. In these plots, the chains are colored using the rainbow schema of the PDB 3D-viewer (where the N- and C-terminal regions are colored blue and red, respectively). ( G ). Evaluation of the intrinsic disorder propensity of rabbit RyR1 (UniProt ID: P11716) by a set of commonly used disorder predictors. Presented disorder profiles were generated by PONDR-FIT (pink curve), PONDR ® VLXT (black curve), PONDR ® VSL2 (green curve), and PONDR ® VL3 (red curve) [ , , , , , ], as well as two tools from the IUPred web server for predicting short and long disordered regions (blue and yellow curves, respectively) . The dark cyan dashed line shows the mean disorder propensity calculated by averaging the disorder profiles of the individual predictors. The light pink shadow around the PONDR ® FIT shows error distribution, whereas the light cyan shadow around the mean disorder curve reflects the distribution of standard deviations. Light gray bars show positions of structurally uncharacterized regions. In these analyses, the predicted intrinsic disorder scores above 0.5 are considered to correspond to the disordered residues/regions, whereas regions with disorder scores between 0.2 and 0.5 are considered flexible.

Article Snippet: Volta Phase Plate (VPP), a type of phase plate technology, yielded the first high resolution cryo-EM 3D structures of hemoglobin [ ], G-protein coupled receptor [ ], streptavidin [ ], and the nucleosome [ ].

Techniques: Single Particle, Cryo-EM Sample Prep, Generated

Journal: International Journal of Molecular Sciences

Article Title: Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

doi: 10.3390/ijms20174186

Figure Lengend Snippet: Single-particle cryo-EM-based structural characterization of the eubacterial and eukaryotic vacuolar-type ATPases (V-ATPases) from Thermus thermophiles (( A ). PDB ID: 5GAR, ) and Saccharomyces cerevisiae (( B ). PDB ID: 3J9T, ), respectively.

Article Snippet: Volta Phase Plate (VPP), a type of phase plate technology, yielded the first high resolution cryo-EM 3D structures of hemoglobin [ ], G-protein coupled receptor [ ], streptavidin [ ], and the nucleosome [ ].

Techniques: Single Particle, Cryo-EM Sample Prep

Journal: International Journal of Molecular Sciences

Article Title: Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

doi: 10.3390/ijms20174186

Figure Lengend Snippet: Three projections of the 3D structure of the deletion mutant of rat TRPV1 resolved by single-particle cryo-EM (PDB ID: 5IRZ, ): ( A ). Cytoplasm view; ( B ). Membrane view; and ( C ). Side view. ( D ). Evaluation of the intrinsic disorder propensity of the full-length rat TRPV1 (UniProt ID: O35433) by a set of commonly used disorder predictors. Presented disorder profiles were generated by PONDR-FIT (pink curve), PONDR ® VLXT (black curve), PONDR ® VSL2 (green curve), and PONDR ® VL3 (red curve) [ , , , , , ], as well as two tools from the IUPred web server for predicting short and long disordered regions (blue and yellow curves, respectively) . The dark cyan dashed line shows the mean disorder propensity calculated by averaging the disorder profiles of the individual predictors. The light pink shadow around the PONDR ® FIT shows error distribution, whereas the light cyan shadow around the mean disorder curve reflects the distribution of the standard deviations. In these analyses, the predicted intrinsic disorder scores above 0.5 are considered to correspond to the disordered residues/regions, whereas regions with disorder scores between 0.2 and 0.5 are considered flexible.

Article Snippet: Volta Phase Plate (VPP), a type of phase plate technology, yielded the first high resolution cryo-EM 3D structures of hemoglobin [ ], G-protein coupled receptor [ ], streptavidin [ ], and the nucleosome [ ].

Techniques: Mutagenesis, Single Particle, Cryo-EM Sample Prep, Generated

Journal: International Journal of Molecular Sciences

Article Title: Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

doi: 10.3390/ijms20174186

Figure Lengend Snippet: Three projections of the 3D structure of the homo-tetrameric Slo2.2 Na + -activated K + channel (chicken KCNT1) resolved by single-particle cryo-EM (PDB ID: 5U70, ): ( A ). Cytoplasm view; ( B ). Membrane view; and ( C ). Side view. ( D ). Evaluation of the intrinsic disorder propensity of the chicken KCNT1 (UniProt ID: Q8QFV0) by a set of commonly used disorder predictors. Presented disorder profiles were generated by PONDR-FIT (pink curve), PONDR ® VLXT (black curve), PONDR ® VSL2 (green curve), and PONDR ® VL3 (red curve) [ , , , , , ], as well as two tools from the IUPred web server for predicting short and long disordered regions (blue and yellow curves, respectively) . The dark cyan dashed line shows the mean disorder propensity calculated by averaging the disorder profiles of the individual predictors. The light pink shadow around the PONDR ® FIT shows the error distribution, whereas the light cyan shadow around the mean disorder curve reflects the distribution of the standard deviations. The light gray bars show positions of structurally uncharacterized regions. In these analyses, the predicted intrinsic disorder scores above 0.5 are considered to correspond to the disordered residues/regions, whereas regions with disorder scores between 0.2 and 0.5 are considered flexible.

Article Snippet: Volta Phase Plate (VPP), a type of phase plate technology, yielded the first high resolution cryo-EM 3D structures of hemoglobin [ ], G-protein coupled receptor [ ], streptavidin [ ], and the nucleosome [ ].

Techniques: Single Particle, Cryo-EM Sample Prep, Generated