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