2017 Nobel Prize in Chemistry
Nature Research congratulates the awardees of the 2017 Nobel Prize in Chemistry - Jacques Dubochet, Joachim Frank and Richard Henderson. Their pioneering work on the use of cryo-electron microscopy to solve high-resolution structures of biomolecules has provided unprecedented insights into the complexity of life. Here, we present a Collection of Research, Methods, Reviews and Comment pieces from Nature Research to celebrate the award.
Single-particle cryo-electron microscopy has enabled the structures of large proteins to be elucidated. This Perspective discusses technological improvements in this technique, focusing particularly on the past decade and likely future developments.
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.
A high-resolution electron cryo-microscopy structure of the rat transient receptor potential (TRP) channel TRPV1 in its ‘closed’ state is presented; the overall structure of this ion channel is found to share some common features with voltage-gated ion channels, although several unique, TRP-specific features are also characterized.
The structures of AMPA receptors in complex with auxiliary proteins are resolved by cryo-electron microscopy, and reveal conformational and permeation pathway changes that are associated with activation and desensitization of ionotropic glutamate receptors.
Electron cryomicroscopy shows structures of three distinct rotational states of the V-ATPase from Saccharomyces cerevisiae.
The 3.7 Å cryo-electron microscopy structure of Zika virus is presented, revealing a typical flavivirus architecture; in contrast to the related flavivirus dengue virus, Zika virus is thermally stable at 40 °C, and this structural stability may be a feature that helps it to survive in semen, saliva and urine.
Single-particle electron cryo-microscopy analysis of the mechanotransduction channel NOMPC reveals that it contains a bundle of four helical spring-shaped ankyrin repeat domains that undergo motion, potentially allowing mechanical movement of the cytoskeleton to be coupled to the opening of the channel.
During protein synthesis within the ribosome, transfer RNAs (tRNAs) move sequentially through different sites as their attached amino acids are transferred onto the growing protein chain. Large conformational movements accompany this process. Here, a staggering 1.9 million electron cryomicroscopy images of the ribosome have been processed to visualize these changes. The results reveal that the ribosome functions as a Brownian machine that couples spontaneous changes driven by thermal energy to directed movement.
From the Laureates
Using electron cryomicroscopy, the closed-state structure of rabbit RyR1 is determined at 4.8 Å resolution; analysis confirms that the RyR1 architecture consists of a six-transmembrane ion channel with a cytosolic α-solenoid scaffold, and suggests a mechanism for Ca2+-induced channel opening.
All living cells translocate proteins across the cell membrane, so the structure of the protein conducting channel was eagerly awaited. The structure of the ribosome-bound protein from E. coli has now been determined, and a model for co-translational protein translocation proposed.
Functional analyses of the ABC-F protein YjjK (EttA) suggest that it acts as a sensor of cellular energy and controls entry into the translational elongation cycle. Using cryo-EM and single-molecule FRET, EttA is shown to bind the ribosomal E site and engage both the L1 stalk and P-site tRNA to restrain ribosomal dynamics.
Although ABC-F proteins represent a ubiquitously distributed type of ATP-binding cassette (ABC) family member across phyla, their biological functions remain poorly characterized. A new study now shows that the bacterial ABC-F protein YjjK (EttA) gates ribosome entry into the translational cycle in an energy-dependent manner.
Reviews, News and Comment
Recent advances in cryo-electron microscopy are enabling researchers to solve protein structures at near-atomic resolutions, expanding the biological applicability of this technique. Michael Eisenstein reports.
Structural biologists are at last living the dream of visualizing macromolecules to uncover their function. But it means integrating different technologies, and that's no easy feat.
Move over X-ray crystallography. Cryo-electron microscopy is kicking up a storm by revealing the hidden machinery of the cell.
This report describes the outcomes of the Data Management Challenges in 3D Electron Microscopy workshop. Key topics discussed include data models, validation and raw-data archiving. The meeting participants agreed that the EMDataBank should take the lead in addressing these issues, and concrete action points were agreed upon that will have a substantial impact on the accessibility of three-dimensional EM data in biology and medicine.
Structures of the heat-sensitive TRPV1 ion channel have been solved using single-particle electron cryo-microscopy, representing a landmark in the use of this technique for structural biology. See Articles p.107 & p.113
G-protein-coupled receptors are biological targets for drug discovery. Developments in cryo-electron microscopy have enabled the solution of the structure of a class B receptor in complex with its signalling protein. Two biologists and a microscopist explain the exciting implications of this work. See Article p.118
An ABC protein that binds the ribosomal exit site suggests a new mechanism for direct regulation of translation in response to changing ATP levels in the cell.
Research, Methods and Protocols
Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM will facilitate determination of three-dimensional structures of smaller, lower-symmetry macromolecular complexes to higher resolution than previously possible.
Using a peptide toxin and small vanilloid agonists as pharmacological probes, high-resolution electron cryo-microscopy structures of rat TRPV1–ligand complexes are solved; these structures highlight conformational differences between TRP and voltage-gated ion channels in their active states, and suggest a dual gating mechanism that may account for the ability of members of the TRP channel superfamily to integrate diverse physiological signals.
Cryo-EM has emerged rapidly as a method for determining high-resolution structures of biological macromolecules. The author of this Commentary discusses just how much better this technology may get and how fast such developments are likely to happen.
A method and software tool, ResMap, for quantifying the local resolution across 3D electron cryo-microscopy density maps is reported.
A 3.7 Å resolution structure for the yeast U4/U6.U5 tri-snRNP, a complex involved in splicing, allows a better appreciation of the architecture of the tri-snRNP, and offers new functional insights into the activation of the spliceosome and the assembly of the catalytic core.
A cryo-electron microscopy structure of the DNA damage repair protein 53BP1 bound to a nucleosome illuminates the way 53BP1 recognizes two types of histone modifications (a methyl group and a ubiquitin moiety), and provides insight into the highly specified recognition and recruitment of 53BP1 to modified chromatin.
A high-resolution structural study sheds light on processes of energy transfer within the photosynthetic water-splitting machinery of plants.
The cryo-electron microscopy structures of yeast initiation complexes containing the transcription factors TBP, TFIIA, TFIIB, TFIIE, and TFIIF and containing either closed or open promoter DNA are reported, providing mechanistic insights into DNA opening and template-strand loading.
Cryo-electron microscopy structural models of the human pre-initiation complex at all major steps of transcription initiation at near atomic-level resolution are presented, providing new mechanistic insights into the processes of promoter melting and transcription-bubble formation, as well as an almost complete proposed structural model of all of the pre-initiation complex components and their interactions with DNA.
Volta phase-plate cryo-electron microscopy reveals the structure of the full-length calcitonin receptor in complex with its peptide ligand and Gαsβγ.
High-resolution structures of tau filaments shed light on the ultrastructure of neurofibrillary lesions in Alzheimer’s disease.
Single particle cryo-EM is commonly used for the structure determination of large complexes. Here, the authors present the 3.2 Å resolution cryo-EM structure of human haemoglobin, which has a molecular weight of 64 kDa.
The atomic structure of human γ-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy.
Using single-particle electron cryomicroscopy, several structures are reported which illuminate the mechanisms of action of the ATPase NSF that disassembles the SNARE complex into individual protein components.
Electron cryomicroscopy reveals the three-dimensional structure of F-actin at a resolution of 3.7 Å in complex with tropomyosin at a resolution of 6.5 Å; the stabilizing interactions and the effects of disease-causing mutants are also investigated.
A tour-de-force of structural biology solves the structure of the macromolecular injection machinery used to deliver a phage genome into a bacterium.
Respirasomes are supercomplexes of mitochondrial electron transport chain complexes that are responsible for cellular respiration and energy production; cryo-electron microscopy structures of mammalian (sheep) respirasomes are presented.
A cryo-EM structure of the human 26S proteasome in a resting state at an average resolution of 3.5 Å reveals details in the interactions between subunits. An additional structure of the proteasome with USP14 bound suggests a mechanism for its activation.
Combined kinetic and cryo-EM analysis of the R197A mutant of GroEL provides insight into the allosteric switching of GroEL, which is at the heart of the chaperonin mechanism.
Using electron cryomicroscopy, the structure of the rabbit RyR1 calcium channel is determined at 6.1 Å resolution in the closed state and 8.5 Å in the open state, revealing how calcium binding to the EF-hand of RyR1 regulates channel opening and facilitates calcium-induced calcium release.
Using electron cryomicroscopy, the structure of the closed-state rabbit ryanodine receptor RyR1 in complex with its modulator FKBP12 is solved at 3.8 Å; in addition to determining structural details of the ion-conducting channel domain, three previously uncharacterized domains help to reveal a molecular scaffold that allows long-range allosteric regulation of channel activities.
In plants, photosystem II forms supercomplexes of core and light-harvesting complexes. Cryo-electron microscopy and single-particle analysis provides a 3D structure of the supercomplex from Arabidopsis at 5.3 Å resolution.
Cryo-electron microscopy of the tripartite MacA–MacB–TolC multidrug transporter.