Featured
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Article |
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
The Ribosolve pipeline combines single-particle cryo-EM, M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination.
- Kalli Kappel
- , Kaiming Zhang
- & Rhiju Das
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Article |
Measurement of atom resolvability in cryo-EM maps with Q-scores
Q-scores provide a quantitative metric for resolvability in cryo-EM maps, and can be used at the atom, residue or macromolecule scale.
- Grigore Pintilie
- , Kaiming Zhang
- & Wah Chiu
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Article |
Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms
A template-free image processing approach automatically detects and classifies membrane-bound protein complexes in cryo-electron tomograms of isolated endoplasmic reticulum and in intact cells.
- Antonio Martinez-Sanchez
- , Zdravko Kochovski
- & Vladan Lučić
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Article |
In situ structure determination at nanometer resolution using TYGRESS
The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.
- Kangkang Song
- , Zhiguo Shang
- & Daniela Nicastro
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Article |
Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu
An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.
- Chi-Min Ho
- , Xiaorun Li
- & Z. Hong Zhou
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Article |
A complete data processing workflow for cryo-ET and subtomogram averaging
An integrated pipeline for processing cryo-ET data implemented in EMAN2 streamlines data processing to minimize human bias, and improves the quality and resolution of resulting macromolecular structures, both in vitro and in cells.
- Muyuan Chen
- , James M. Bell
- & Steven J. Ludtke
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Article |
Real-time cryo-electron microscopy data preprocessing with Warp
The user-friendly software tool Warp enables automated, on-the-fly preprocessing of cryo-EM data, including motion correction, defocus estimation, particle picking and image denoising.
- Dimitry Tegunov
- & Patrick Cramer
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Article |
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
The challenge of accurate particle picking in cryo-EM analysis is addressed with Topaz, a neural-network-based algorithm that shows advantages over other tools, especially in picking unusually shaped particles.
- Tristan Bepler
- , Andrew Morin
- & Bonnie Berger
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News & Views |
Electrons see the light
Focused laser light can manipulate the phase of electrons and solve the long-standing phase contrast conundrum in electron microscopy.
- Radostin Danev
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Article |
A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue
A technique to ‘lift out’ samples of interest from high-pressure-frozen specimens expands applications of cryo-electron tomography to multicellular organisms and tissue.
- Miroslava Schaffer
- , Stefan Pfeffer
- & Juergen M. Plitzko
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Article |
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning
Emap2sec uses a deep convolutional neural network to assign protein secondary structures in intermediate-resolution (5–10 Å) cryo-EM maps.
- Sai Raghavendra Maddhuri Venkata Subramaniya
- , Genki Terashi
- & Daisuke Kihara
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Perspective |
Software tools for automated transmission electron microscopy
Py-EM and SerialEM enable automated microscope control for high-throughput data acquisition in diverse transmission electron microscopy imaging experiments.
- Martin Schorb
- , Isabella Haberbosch
- & David N. Mastronarde
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Perspective |
The cryo-EM method microcrystal electron diffraction (MicroED)
This paper reviews the cryo-EM technique of microcrystal electron diffraction (MicroED), providing a broad overview of the technique, the unique structures determined, and the opportunities for future development.
- Brent L. Nannenga
- & Tamir Gonen
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Editorial |
Challenges for cryo-EM
Two community challenges assess the correctness of cryo-EM structures; future challenges should help determine the most appropriate structure validation methods.
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Article |
A particle-filter framework for robust cryo-EM 3D reconstruction
A particle-filter algorithm for single-particle cryo-electron microscopy, implemented in a tool called THUNDER, provides high-dimensional parameter estimation, improving the obtainable resolution for several protein structures.
- Mingxu Hu
- , Hongkun Yu
- & Xueming Li
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Brief Communication |
A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
A fully automated method for modeling protein and protein–RNA complex structure from cryo-EM data, requiring minimal user intervention, is described.
- Thomas C. Terwilliger
- , Paul D. Adams
- & Oleg V. Sobolev
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Article |
De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes
DRRAFTER, a method for RNA modeling into cryo-EM maps, generates accurate models for diverse RNA–protein complexes.
- Kalli Kappel
- , Shiheng Liu
- & Rhiju Das
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Article |
emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging
A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures.
- Benjamin A. Himes
- & Peijun Zhang
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This Month |
Bridget Carragher
Speeding up spot-to-plunge in cryo-EM and how to keep a lab talking.
- Vivien Marx
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Brief Communication |
Reducing effects of particle adsorption to the air–water interface in cryo-EM
Reducing the length of time that protein particles spend on a sample grid prior to freezing mitigates deleterious effects caused by particle adsorption to the air–water interface in single-particle cryo-EM.
- Alex J. Noble
- , Hui Wei
- & Bridget Carragher
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Research Highlight |
Taking inventory with shotgun EM
The combination of single-particle electron microscopy and mass spectrometry shows potential for surveys of both the structure and the identity of protein complexes in the cell.
- Allison Doerr
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Tools in Brief |
cisTEM software for cryo-EM
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Tools in Brief |
Local resolution of cryo-EM maps with MonoRes
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Methods in Brief |
Improving the efficiency of cryo-EM
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Brief Communication |
Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV
Cryo-EM-based structure determination of macromolecular complexes at near-atomic resolution is possible using a mid-range 200-keV transmission electron microscope instrument.
- Mark A Herzik Jr
- , Mengyu Wu
- & Gabriel C Lander
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Research Highlights |
Seeing DNA
DNA and chromatin structures can be visualized in situ with electron tomography.
- Zachary J Lapin
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Brief Communication |
Addressing preferred specimen orientation in single-particle cryo-EM through tilting
The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.
- Yong Zi Tan
- , Philip R Baldwin
- & Dmitry Lyumkis
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Methods in Brief |
Single-protein detection by cryo-EM
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Research Highlights |
Zooming into the larval zebrafish brain
A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure–function analyses of the animals' neural circuitry.
- Nina Vogt
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Brief Communication |
RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps
RosettaES, an algorithm that uses a fragment-based sampling strategy, improves macromolecular structure modeling from cryo-EM data at 3–5-Å resolution.
- Brandon Frenz
- , Alexandra C Walls
- & Frank DiMaio
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Tools in Brief |
GPCR function insights by cryo-EM
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Research Highlights |
Protein holography
Low-energy holography enables imaging single proteins and protein complexes.
- Zachary J Lapin
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Correspondence |
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.
- Shawn Q Zheng
- , Eugene Palovcak
- & David A Agard
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Brief Communication |
Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED
Fragmentation of large, imperfect crystals into nanocrystals by sonication, vortexing, or vigorous pipetting facilitates atomic-resolution analysis by the cryo-EM method MicroED.
- M Jason de la Cruz
- , Johan Hattne
- & Tamir Gonen
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Article |
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
- Ali Punjani
- , John L Rubinstein
- & Marcus A Brubaker
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Method to Watch |
Cryo-electron tomography
Cryo-electron tomography may facilitate in situ structural biology on a proteomic scale.
- Allison Doerr
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Research Highlights |
Colorful electron microscopy
A multicolor approach specifically labels multiple targets in electron microscopy images.
- Rita Strack
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Advertising Feature: Application Note |
Recent developments in FEI's in situ cryo-electron tomography workflow
- Alexander Rigort
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Correspondence |
The democratization of cryo-EM
- David I Stuart
- , Sriram Subramaniam
- & Nicola G A Abrescia
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Methods in Brief |
Cryo-EM with the Volta phase plate
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Correspondence |
EMPIAR: a public archive for raw electron microscopy image data
- Andrii Iudin
- , Paul K Korir
- & Ardan Patwardhan
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Article |
A saposin-lipoprotein nanoparticle system for membrane proteins
A saposin protein–lipid nanoparticle system stabilizes diverse, fragile membrane proteins in a lipid environment for structural and functional studies.
- Jens Frauenfeld
- , Robin Löving
- & Pär Nordlund
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Editorial |
Method of the Year 2015
The end of 'blob-ology': single-particle cryo-electron microscopy (cryo-EM) is now being used to solve macromolecular structures at high resolution.
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Primer |
Single-particle cryo-electron microscopy
A brief overview of how to solve a macromolecular structure using single-particle cryo-electron microscopy (cryo-EM).
- Allison Doerr
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Historical Commentary |
The development of cryo-EM into a mainstream structural biology technique
Single-particle cryo-electron microscopy (cryo-EM) has emerged over the last two decades as a technique capable of studying the structure of challenging systems. The author of this Commentary discusses some of the major historical landmarks in cryo-EM that have led to its present success.
- Eva Nogales