Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation

Structural basis of ribosomal RNA transcription regulation

(2021) Yeonoh Shin et al.   Nature Communications

Structural basis for transcription complex disruption by the Mfd translocase

(2021) Jin Young Kang et al.   eLife

Molecular basis for control of antibiotic production by a bacterial hormone

(2021) Shanshan Zhou et al.   NATURE

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

(2021) Ellen D. Zhong et al.   NATURE METHODS

Understanding the invisible hands of sample preparation for cryo-EM

(2021) Giulia Weissenberger et al.   NATURE METHODS

Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

(2021) Christopher R. Horne et al.   Nature Communications

High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

(2021) Betty Ha et al.   Nature Communications

Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning

(2021) Xiao Wang et al.   Nature Communications

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator

(2021) Yang Yang et al.   Nature Communications

Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution

(2021) Marta Kulik et al.   Frontiers in Molecular Biosciences

Structural basis of copper-efflux-regulator-dependent transcription activation

(2021) Wei Shi et al.   iScience

N-Acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization

(2021) Michael J. Currie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

(2021) Ali Punjani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7

(2021) Mirjana Lilic et al.   MOLECULAR CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture

(2021) Adrian M Bandera et al.   NUCLEIC ACIDS RESEARCH

Structural basis of transcription activation by the global regulator Spx

(2021) Jing Shi et al.   NUCLEIC ACIDS RESEARCH

The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus

(2020) David Coombes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐Electron Microscopy Maps

(2020) Philipp Mostosi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Stepwise Promoter Melting by Bacterial RNA Polymerase

(2020) James Chen et al.   MOLECULAR CELL

Visualization of two architectures in class-II CAP-dependent transcription activation

(2020) Wei Shi et al.   PLOS BIOLOGY

Time-resolved cryo-EM using Spotiton

(2020) Venkata P. Dandey et al.   NATURE METHODS

Single molecule mass photometry of nucleic acids

(2020) Yiwen Li et al.   NUCLEIC ACIDS RESEARCH

Structural interpretation of cryo-EM image reconstructions

(2020) Maximilian Beckers et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins

(2020) Tural Aksel et al.   NATURE BIOTECHNOLOGY

CueR activates transcription through a DNA distortion mechanism

(2020) Chengli Fang et al.   Nature Chemical Biology

Structural basis for transcription inhibition by E. coli SspA

(2020) Fulin Wang et al.   NUCLEIC ACIDS RESEARCH

Structural basis of Mfd-dependent transcription termination

(2020) Jing Shi et al.   NUCLEIC ACIDS RESEARCH

General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM

(2020) Feng Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure–function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay

(2020) Glenn C. Capodagli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-wavelength analytical ultracentrifugation as a tool to characterise protein–DNA interactions in solution

(2020) Christopher R. Horne et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase

(2020) Brent De Wijngaert et al.   MOLECULAR CELL

The antibiotic sorangicin A inhibits promoter DNA unwinding in aMycobacterium tuberculosisrifampicin-resistant RNA polymerase

(2020) Mirjana Lilic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription

(2020) Chengli Fang et al.   Nature Communications

Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

(2020) Timothy P. Newing et al.   Nature Communications

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

(2020) Tomáš Kouba et al.   Nature Communications

Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding

(2019) Hande Boyaci et al.   NATURE

Bioactive Functionalized Monolayer Graphene for High-Resolution Cryo-Electron Microscopy

(2019) Nan Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Challenges and opportunities in cryo-EM single-particle analysis

(2019) Dmitry Lyumkis   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation

(2019) Mo’men Abdelkareem et al.   MOLECULAR CELL

Multifunctional graphene supports for electron cryomicroscopy

(2019) Katerina Naydenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein denaturation at the air-water interface and how to prevent it

(2019) Edoardo D'Imprima et al.   eLife

Principles for Integrative Structural Biology Studies

(2019) Michael P. Rout et al.   CELL

cryo_fit: Democratization of Flexible Fitting for Cryo-EM

(2019) Doo Nam Kim et al.   JOURNAL OF STRUCTURAL BIOLOGY

AgarFix: Simple and accessible stabilization of challenging single-particle cryo-EM specimens through crosslinking in a matrix of agar

(2019) Klaudia Adamus et al.   JOURNAL OF STRUCTURAL BIOLOGY

Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

(2019) Rune Thomas Kidmose et al.   IUCrJ

Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

(2019) Emeka Nwanochie et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase

(2019) Alexis Jaramillo Cartagena et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism

(2019) Christopher R. Horne et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps

(2019) Eman Alnabati et al.   MOLECULES

Developments, applications, and prospects of cryo‐electron microscopy

(2019) Xu Benjin et al.   PROTEIN SCIENCE

E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation

(2019) James Chen et al.   eLife

X-rays in the Cryo-Electron Microscopy Era: Structural Biology’s Dynamic Future

(2018) Susannah C. Shoemaker et al.   BIOCHEMISTRY

Streptavidin Affinity Grids for cryo-EM

(2018) Robert M. Glaeser et al.   BIOPHYSICAL JOURNAL

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators

(2018) Jin Young Kang et al.   CELL

The cryo-EM resolution revolution and transcription complexes

(2018) Jonas Hanske et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Cryo-EM structure ofEscherichia coliσ70RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation

(2018) Anoop Narayanan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation

(2018) Dariush Ashtiani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Spotiton: New features and applications

(2018) Venkata P. Dandey et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation

(2018) Robert Glyde et al.   MOLECULAR CELL

Architecture of an HIV-1 reverse transcriptase initiation complex

(2018) Kevin P. Larsen et al.   NATURE

Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors

(2018) Ernesto Perez-Rueda et al.   PLoS One

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

cisTEM, user-friendly software for single-particle image processing

(2018) Timothy Grant et al.   eLife

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Approaches to altering particle distributions in cryo-electron microscopy sample preparation

(2018) Ieva Drulyte et al.   Acta Crystallographica Section D-Structural Biology

Reducing effects of particle adsorption to the air–water interface in cryo-EM

(2018) Alex J. Noble et al.   NATURE METHODS

Time-resolved cryo-electron microscopy: Recent progress

(2017) Joachim Frank   JOURNAL OF STRUCTURAL BIOLOGY

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

(2017) Yong Zi Tan et al.   NATURE METHODS

Structural basis of bacterial transcription activation

(2017) Bin Liu et al.   SCIENCE

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

(2017) Elizabeth A Hubin et al.   eLife

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

(2016) Eva Nogales et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology

(2016) Rebecca F. Thompson et al.   METHODS

Local and global regulation of transcription initiation in bacteria

(2016) Douglas F. Browning et al.   NATURE REVIEWS MICROBIOLOGY

Structures ofE.coliσS-transcription initiation complexes provide new insights into polymerase mechanism

(2016) Bin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Primer to Single-Particle Cryo-Electron Microscopy

(2015) Yifan Cheng et al.   CELL

Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity

(2015) Eva Nogales et al.   MOLECULAR CELL

ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space

(2015) Ashwin Chari et al.   NATURE METHODS

De novo protein structure determination from near-atomic-resolution cryo-EM maps

(2015) Ray Yu-Ruei Wang et al.   NATURE METHODS

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

(2015) S. J. Philips et al.   SCIENCE

Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy

(2015) Holger Stark et al.   Microscopy

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

Ultrastable gold substrates for electron cryomicroscopy

(2014) C. J. Russo et al.   SCIENCE

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

(2013) José Ramón Lopéz-Blanco et al.   JOURNAL OF STRUCTURAL BIOLOGY

Mutation in the C-Di-AMP Cyclase dacA Affects Fitness and Resistance of Methicillin Resistant Staphylococcus aureus

(2013) Vanina Dengler et al.   PLoS One

High-Throughput Thermal Scanning for Protein Stability: Making a Good Technique More Robust

(2013) Shane A. Seabrook et al.   ACS Combinatorial Science

Activating Transcription in Bacteria

(2012) David J. Lee et al.   Annual Review of Microbiology

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Structural characterization of proteins and complexes using small-angle X-ray solution scattering

(2010) Haydyn D.T. Mertens et al.   JOURNAL OF STRUCTURAL BIOLOGY

RNA polymerase and transcription elongation factor Spt4/5 complex structure

(2010) B. J. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional activation of MerR family promoters in Cupriavidus metallidurans CH34

(2008) Daniel J. Julian et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

RNA polymerase: A nexus of gene regulation

(2008) John D. Helmann   METHODS

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE