Advanced Electron Microscopy Techniques and Applications

CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology

CryoDataBot automates the creation of high-quality cryoEM datasets for AI-driven structural biology, improving training efficiency and enabling flexible dataset customization.

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

This paper presents a workflow for cryo-EM structure determination of small proteins using heterogeneous ab initio reconstruction, successfully solving structures of three small proteins with resolutions below 5 Å.

How many (distinguishable) classes can we identify in Single Particle Analysis?

The paper investigates using p-values to estimate the number of distinguishable classes in cryoEM data by testing if classifications differ from random partitions.

Genetically Encoded FerriTag as a Specific Label for Cryo-Electron Tomography

This paper introduces a genetically encoded FerriTag system for labeling target proteins in live cells for cryo-electron tomography, enabling precise localization with high contrast.

Determination of the water network surrounding the type I pilus from E. coli by cryo-electron microscopy

The paper improves the resolution of the Cryo-EM structure of E. coli type I pilus, enabling detailed analysis of water molecule interactions and subunit stabilization.

Bridging the resolution gap in cryo-CLEM by introducing cryo-SXT: cryo-CLXEM

This paper introduces cryo-SXT as an intermediate technique to bridge the resolution gap in cryo-CLEM by providing 3D cellular context to cryo-ET datasets.

Validation of 3D cryoEM single particle reconstruction correctness and handedness with Ewald's sphere correction

This paper introduces a method to validate 3D cryoEM reconstructions by separating scattering contributions into real and imaginary components to determine handedness and assess reconstruction quality.

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

This paper combines cryo-EM and FIB-SIMS to map sub-cellular chemical distributions in bacteria, revealing pollutant storage in phase-separated aggregates.

Laser Flash Melting Cryo-EM Samples to Overcome Preferred Orientation

This paper introduces a method to reduce preferred orientation in cryo-EM samples using laser flash melting and revitrification, improving protein structure determination.

Leopard-EM: An extensible 2DTM package to accelerate in situ structural biology

Leopard-EM accelerates in situ cryo-EM analysis by providing a modular 2DTM framework that improves ribosome detection and enables single-molecule resolution of rotation states.

Volumetric Denoising: An Approach to Boost Acquisition and Downstream Analysis of Volume Electron Microscopy

This paper develops a volumetric denoising approach to improve VEM acquisition speed and downstream analysis by optimizing resolution and noise handling.

Validation of helical symmetry parameters in EMDB

The paper validates helical symmetry parameters in EMDB by identifying and correcting inconsistencies between parameters and density maps.

Magellon - an extensible platform for cryo-EM data visualization, management, and processing

Magellon provides a flexible and scalable cryo-EM platform with microservices architecture for data management, processing, and visualization.

Cryogenic light microscopy with Angstrom precision deciphers structural conformations of PIEZO1

This study uses cryogenic light microscopy to determine three conformational states of PIEZO1 in the cell membrane, revealing structural changes associated with channel opening.

Optimising the tilt-increment for in situ cryo-electron tomography

This study evaluates tilt increments in cryo-ET to find the optimal balance between image quality and radiation damage, recommending 3 degrees as the best increment.

PickET: An unsupervised method for localizing macromolecules in cryo-electron tomograms

PickET localizes macromolecules in cryo-ET tomograms without expert annotations or prior structures, showing effectiveness across diverse datasets.

Off-Target Structural Insights: ArnA and AcrB in Bacterial Membrane Protein Cryo-EM Analysis

The paper uses cryo-EM to analyze membrane proteins, revealing unexpected high-resolution structures of ArnA and AcrB instead of the intended FtsH and YidC complex.

CryoEM Structures of Antibodies Elicited by Germline-Targeting HIV MPER Epitope-Scaffolds

This paper uses cryoEM to analyze antibody-antigen interactions with HIV MPER-GT immunogens, revealing binding patterns and epitopes that inform antigen optimization.

Di-Gluebodies as covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures

The paper introduces Di-Gluebodies, covalently-dimerized nanobodies, to improve cryo-EM structure determination of small proteins by providing rigidity and modularity.

Cryo-EM protein structure without purification

This paper demonstrates cryo-EM can solve protein structures directly from cell-free expression mixtures with minimal purification, reducing time and reagent use.

Cryogenic electron tomography and elemental analysis of mitochondrial granules in human retinal ganglion cells

The paper uses cryoEELS and cryoET to study calcium distribution in mitochondria of human retinal ganglion cells under calcifying conditions, revealing mitochondrial calcification.

Sub-3 A resolution protein structure determination by single-particle cryo-EM at 100 keV

This paper demonstrates that a 100 keV cryo-TEM with advanced components can achieve sub-3 Å resolution structures of various proteins and viruses.

AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact

The paper introduces AIVE, an AI-assisted method for segmenting membrane boundaries in vEM data, revealing a new type of mitochondrial contact called intrusions.

Cryo-EM structure and polar assembly of the PS2 S-layer of Corynebacterium glutamicum

The paper determines the atomic structure of the PS2 S-layer from Corynebacterium glutamicum using cryo-EM and shows its polar assembly mechanism and phylogenetic distribution.

Recognizing amino acid sidechains in a medium resolution cryo-electron density map

EMSequenceFinder accurately assigns amino acid sequences to cryo-EM map backbone fragments, outperforming existing methods in resolution 3-10 Å maps.

Unsupervised learning of structural variability in cryo-EM data using normal mode analysis of deformable atomic models

The paper introduces an unsupervised method to analyze structural variability in cryo-EM data by deforming atomic models using normal mode analysis directly against 2D data, improving accuracy and interpretability.

Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation

This paper introduces EMERALD-ID, a method for identifying small molecules in cryo-EM data, achieving 43% exact identification and 66% close identification of common ligands.

VitriFlex: An Open-Source, Modular, and Customizable Robotic Platform for Cryo-EM Grid Preparation

VitriFlex is an open-source robotic platform for cryo-EM grid preparation that enables customizable and high-resolution grid production through modular design and programmable control.

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

The paper presents a cryo-EM conformational heterogeneity challenge to evaluate and improve methods for analyzing molecular motions in heterogeneous samples.

Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO

This paper introduces TANGO, a framework for analyzing spatial arrangements of particles in cryo-ET using point cloud descriptors, enabling rotationally invariant feature extraction and exploratory analysis of cellular structures.