Posts Tagged ‘cryoEM’

Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise | PNAS

September 28, 2019

Avoiding the pitfalls of single-particle #cryoEM: Einstein from noise https://www.PNAS.org/content/110/45/18037 A great paper, explaining in simple terms how you can fool yourself with fancy computer algorithms. However, perhaps it’s a bit too honest – only a Nobelist could write this!

Analysis of discrete local variability and structural covariance in macromolecular assemblies using cryo-EM and focused classification

June 21, 2019

http://grigoriefflab.janelia.org/node/6031
https://www.sciencedirect.com/science/article/abs/pii/S0304399118302663?via%3Dihub

Single-protein detection in crowded molecular environments in cryo-EM images | eLife

June 21, 2019

https://elifesciences.org/articles/25648

Cryo-EM structure of substrate-bound human telomerase holoenzyme | Nature

April 28, 2018

#CryoEM structure of substrate-bound human telomerase holoenzyme https://www.Nature.com/articles/s41586-018-0062-x Quote: “2 flexibly RNA-tethered lobes: the catalytic core (w/ #TERT & conserved motifs of telomerase RNA) & an H/ACA RNP”

What to expect in 2018: science in the new year

January 13, 2018

What to expect in ’18: science in the new year
https://www.Nature.com/articles/d41586-018-00009-5 Insights from cancer & ancient #genomes. Cures from #CRISPR. Progress in
#OpenAccess. Also, lots on outer space. But nothing on #cryoEM, #DeepLearning, #QuantumComputing or the brain connectome. HT @OBahcall

Cryo-Electron Tomography at Yale

December 23, 2017

http://www.cryoet.org/

Cutting Edge: Building bridges between cellular and molecular structural biology

December 22, 2017

Cutting Edge: Building bridges between cellular & mol. structural biology https://ELIFEsciences.org/articles/25835 quote: “The use of structured biological #annotation is not common practice in
#cryoEM…[but] by the end of the meeting there was a clearer appreciation of the importance of [this]”

QT:{{”
As previously explained, structured biological annotation is the association of data with identifiers and ontologies taken from well-established bioinformatics resources. The use of structured biological annotation is not common practice in the electron microscopy or structural biology communities. Therefore, ontology experts were invited to the workshop to explain why these are useful and what resources and tools are available for assigning annotations. Use-cases such as mouse imaging data helped to explain the principles and practice of structured biological annotation. By the end of the meeting there was a clearer appreciation of the importance of structured biological annotation for searching and linking imaging data across different scales, between different imaging and structural databases and with other bioinformatics resources.”
“}}

Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating – ScienceDirect

November 30, 2017

QT:{{”
• Find 3.8 Å resolution cryo-EM structure of the ∼200 kDa magnesium channel CorA • Mg2+-free CorA exhibits dramatic loss of symmetry in the cytoplasmic domain …
• Inter-subunit Mg2+ is important for stabilizing the closed state of CorA “}}

#CryoEM Structures of the Mg++ Channel CorA Reveal Symmetry Break upon Gating https://www.ScienceDirect.com/science/article/pii/S0092867415017195 In closed conformation: 5 identical subunits arranged tightly around 5-fold axis & pore. In open: they lose bridging ions & open to differing degrees with helix-hinging motions.

Matthies D1, Dalmas O2, Borgnia MJ1, Dominik PK2, Merk A1, Rao P1, Reddy BG2, Islam S2, Bartesaghi A1, Perozo E3, Subramaniam S4. Cell. 2016 Feb 11;164(4):747-56. doi: 10.1016/j.cell.2015.12.055.

Atomic structure of the entire mammalian mitochondrial complex I | Nature

November 25, 2017

Atomic structure of the entire mammalian mitochondrial complex I https://www.Nature.com/articles/nature19794 Synthesizing #cryoEM w/ (high-FP) cross-linking data to gets a 3.9A structure w/ 78 helices

Fiedorczuk, K., Letts, J.A., Degliesposti, G., Kaszuba, K., Skehel, M., Sazanov, L.A. (2016) Atomic structure of the entire mammalian mitochondrial complex I. Nature 538; 406-410.

related to:
• Letts, J.A., Fiedorczuk, K., Sazanov, L.A. (2016) The architecture of respiratory supercomplexes. Nature 537; 644-648.

Quantifying the local resolution of cryo-EM density maps | Nature Methods

November 14, 2017

Quantifying the local resolution of #cryoEM density maps
https://www.Nature.com/articles/nmeth.2727 “Theory…based on the following idea: a L Angstrom feature exists at a pt…if a 3D local sinusoid of wavelength L is statistically detectable above noise at that point.”

QT:{{”
We propose a mathematical theory and an efficient algorithm for measuring local resolution that address all of the above limitations. The theory (Online Methods) is based on the following idea: a λ-Å feature exists at a point in the volume if a three-dimensional (3D) local sinusoid of wavelength λ is statistically detectable above noise at that point. A likelihood-ratio hypothesis test of the local sinusoid versus noise can detect this feature at a given P value (typically P = 0.05). We define the local resolution at a point as the smallest λ at which the local sinusoid is detectable, and we account for multiple testing with an FDR procedure.
“}}