The integrative role of cryo electron microscopy in molecular and cellular structural biology

SharpViSu: integrated analysis and segmentation of super-resolution microscopy data

(2016) Leonid Andronov et al.   BIOINFORMATICS

Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy

(2016) Jan Arnold et al.   BIOPHYSICAL JOURNAL

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

(2016) Alan Merk et al.   CELL

Cellular structural biology as revealed by cryo-electron tomography

(2016) Rossitza N. Irobalieva et al.   JOURNAL OF CELL SCIENCE

In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology

(2016) Shoh Asano et al.   JOURNAL OF MOLECULAR BIOLOGY

Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography

(2016) Jesús G. Galaz-Montoya et al.   JOURNAL OF STRUCTURAL BIOLOGY

An improved cryo-FIB method for fabrication of frozen hydrated lamella

(2016) Jianguo Zhang et al.   JOURNAL OF STRUCTURAL BIOLOGY

A new method for vitrifying samples for cryoEM

(2016) Ivan Razinkov et al.   JOURNAL OF STRUCTURAL BIOLOGY

Cryo electron microscopy to determine the structure of macromolecular complexes

(2016) Marta Carroni et al.   METHODS

The collection of MicroED data for macromolecular crystallography

(2016) Dan Shi et al.   Nature Protocols

3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

(2016) Eugene Y.D. Chua et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM of viruses and vaccine design

(2016) Lesley A. Earl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

Architecture of the symmetric core of the nuclear pore

(2016) D. H. Lin et al.   SCIENCE

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

(2016) J. Kosinski et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Architecture of the type IVa pilus machine

(2016) Yi-Wei Chang et al.   SCIENCE

2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition

(2016) S. Banerjee et al.   SCIENCE

Towards an optimum design for thin film phase plates

(2016) Daniel Rhinow   ULTRAMICROSCOPY

Volta phase plate cryo-EM of the small protein complex Prx3

(2016) Maryam Khoshouei et al.   Nature Communications

Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation

(2016) Franck Martin et al.   Nature Communications

Structure–function insights reveal the human ribosome as a cancer target for antibiotics

(2016) Alexander G. Myasnikov et al.   Nature Communications

ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy

(2016) Leonid Andronov et al.   Scientific Reports

Protein complexes in focus

(2016) Robert M Glaeser   eLife

Cryo-EM single particle analysis with the Volta phase plate

(2016) Radostin Danev et al.   eLife

EIGER detector: application in macromolecular crystallography

(2016) Arnau Casanas et al.   Acta Crystallographica Section D-Structural Biology

Developments in cryo-electron tomography for in situ structural analysis

(2015) Anna Dubrovsky et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data

(2015) J.M. Carazo et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Cryo-focused-ion-beam applications in structural biology

(2015) Alexander Rigort et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes

(2015) Brice Beinsteiner et al.   BIOINFORMATICS

Structural Basis of Vesicle Formation at the Inner Nuclear Membrane

(2015) Christoph Hagen et al.   CELL

Fast and precise targeting of single tumor cellsin vivoby multimodal correlative microscopy

(2015) Matthia A. Karreman et al.   JOURNAL OF CELL SCIENCE

FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM

(2015) Maarten Kuijper et al.   JOURNAL OF STRUCTURAL BIOLOGY

The influence of frame alignment with dose compensation on the quality of single particle reconstructions

(2015) John M. Spear et al.   JOURNAL OF STRUCTURAL BIOLOGY

A focused ion beam milling and lift-out approach for site-specific preparation of frozen-hydrated lamellas from multicellular organisms

(2015) Julia Mahamid et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of the human 80S ribosome

(2015) Heena Khatter et al.   NATURE

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

The complete structure of the 55S mammalian mitochondrial ribosome

(2015) B. J. Greber et al.   SCIENCE

Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy

(2015) Hstau Y. Liao et al.   STRUCTURE

Structural Dynamics of Ribosome Subunit Association Studied by Mixing-Spraying Time-Resolved Cryogenic Electron Microscopy

(2015) Bo Chen et al.   STRUCTURE

Towards an optimum design for electrostatic phase plates

(2015) Andreas Walter et al.   ULTRAMICROSCOPY

Structural analysis of herpes simplex virus by optical super-resolution imaging

(2015) Romain F. Laine et al.   Nature Communications

Structure of a bacterial type III secretion system in contact with a host membrane in situ

(2015) Andrea Nans et al.   Nature Communications

Live cell immunogold labelling of RNA polymerase II

(2015) Igor Orlov et al.   Scientific Reports

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6

(2015) Timothy Grant et al.   eLife

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Programming new geometry restraints: parallelity of atomic groups

(2015) Oleg V. Sobolev et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Automated data collection in single particle electron microscopy

(2015) Yong Zi Tan et al.   Microscopy

Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy

(2015) Doory Kim et al.   PLoS One

Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution

(2014) Anna Löschberger et al.   JOURNAL OF CELL SCIENCE

Focused ion beam scanning electron microscopy in biology

(2014) C. KIZILYAPRAK et al.   JOURNAL OF MICROSCOPY

Cryo-Electron Microscopy Structure of Lactococcal Siphophage 1358 Virion

(2014) S. Spinelli et al.   JOURNAL OF VIROLOGY

In-Focus Electrostatic Zach Phase Plate Imaging for Transmission Electron Microscopy with Tunable Phase Contrast of Frozen Hydrated Biological Samples

(2014) Nicole Frindt et al.   MICROSCOPY AND MICROANALYSIS

Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages

(2014) Wei Dai et al.   Nature Protocols

Purification, characterization and crystallization of the human 80S ribosome

(2014) Heena Khatter et al.   NUCLEIC ACIDS RESEARCH

Conformation transitions of eukaryotic polyribosomes during multi-round translation

(2014) Zhanna A. Afonina et al.   NUCLEIC ACIDS RESEARCH

Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study

(2014) Zhanna A. Afonina et al.   NUCLEIC ACIDS RESEARCH

Volta potential phase plate for in-focus phase contrast transmission electron microscopy

(2014) R. Danev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autofocused 3D Classification of Cryoelectron Subtomograms

(2014) Yuxiang Chen et al.   STRUCTURE

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

(2014) G. McMullan et al.   ULTRAMICROSCOPY

The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning

(2014) Massimiliano Maletta et al.   Nature Communications

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

(2014) Alexander G. Myasnikov et al.   Nature Communications

Beam-induced motion correction for sub-megadalton cryo-EM particles

(2014) Sjors HW Scheres   eLife

Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector

(2014) Matteo Allegretti et al.   eLife

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

(2014) Wilson Wong et al.   eLife

Imaging protein three-dimensional nanocrystals with cryo-EM

(2013) Igor Nederlof et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems

(2013) Paul D. Adams et al.   Annual Review of Biophysics

Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms

(2013) Min Xu et al.   BIOINFORMATICS

Structural biology in situ—the potential of subtomogram averaging

(2013) John AG Briggs   CURRENT OPINION IN STRUCTURAL BIOLOGY

Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography

(2013) Elizabeth Villa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Cryo-electron tomography: The challenge of doing structural biology in situ

(2013) Vladan Lučić et al.   JOURNAL OF CELL BIOLOGY

Likelihood-based classification of cryo-EM images using FREALIGN

(2013) Dmitry Lyumkis et al.   JOURNAL OF STRUCTURAL BIOLOGY

Maximizing the potential of electron cryomicroscopy data collected using direct detectors

(2013) David Veesler et al.   JOURNAL OF STRUCTURAL BIOLOGY

Quantitative characterization of electron detectors for transmission electron microscopy

(2013) Rachel S. Ruskin et al.   JOURNAL OF STRUCTURAL BIOLOGY

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

(2013) Xueming Li et al.   NATURE METHODS

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

(2013) A. Simonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases

(2013) D. Eiler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging

(2013) A. Szymborska et al.   SCIENCE

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

(2013) Xiao-chen Bai et al.   eLife

Exploiting structure similarity in refinement: automated NCS and target-structure restraints inBUSTER

(2012) Oliver S. Smart et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Cryo-electron microscopy - a primer for the non-microscopist

(2012) Jacqueline L. S. Milne et al.   FEBS Journal

Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging

(2012) Gabriel A. Frank et al.   JOURNAL OF STRUCTURAL BIOLOGY

Beam-induced motion of vitrified specimen on holey carbon film

(2012) Axel F. Brilot et al.   JOURNAL OF STRUCTURAL BIOLOGY

A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography

(2012) Oleg Kuybeda et al.   JOURNAL OF STRUCTURAL BIOLOGY

Cryo-EM structure of the mature dengue virus at 3.5-Å resolution

(2012) Xiaokang Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Movies of Ice-Embedded Particles Enhance Resolution in Electron Cryo-Microscopy

(2012) Melody G. Campbell et al.   STRUCTURE

Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography

(2012) Alexander G. Myasnikov et al.   ULTRAMICROSCOPY

Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA

(2011) Igor Orlov et al.   EMBO JOURNAL

Clustering and variance maps for cryo-electron tomography using wedge-masked differences

(2011) John M. Heumann et al.   JOURNAL OF STRUCTURAL BIOLOGY

In vivo virus structures: Simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography

(2011) Kang Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

(2011) Zheng Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector

(2011) Chitra Rajendran et al.   JOURNAL OF SYNCHROTRON RADIATION

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Imaging of organelles by electron microscopy reveals protein-protein interactions in mitochondria and chloroplasts

(2010) Natalya V. Dudkina et al.   FEBS LETTERS

Maximum likelihood based classification of electron tomographic data

(2010) Michael Stölken et al.   JOURNAL OF STRUCTURAL BIOLOGY

Discrete Structure of an RNA Folding Intermediate Revealed by Cryo-electron Microscopy

(2010) Nathan J. Baird et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Three-Dimensional Organization of Polyribosomes in Intact Human Cells

(2010) Florian Brandt et al.   MOLECULAR CELL

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

(2010) Niels Fischer et al.   NATURE

Crystal Structure of the Eukaryotic Ribosome

(2010) A. Ben-Shem et al.   SCIENCE

Zernike Phase Contrast Cryo-Electron Microscopy and Tomography for Structure Determination at Nanometer and Subnanometer Resolutions

(2010) Kazuyoshi Murata et al.   STRUCTURE

Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM

(2009) J. Z. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detective quantum efficiency of electron area detectors in electron microscopy

(2009) G. McMullan et al.   ULTRAMICROSCOPY

Structure of the 30S translation initiation complex

(2008) Angelita Simonetti et al.   NATURE