Collection |

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.
 

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Transient receptor potential (TRP) channels are sensors for a wide range of physical and chemical stimuli. In the first of a pair of related papers, Maofu Liao et al. solve the high-resolution electron cryo-microscopy structure of rat TRPV1, the receptor for capsaicin (a pungent agent from chili peppers), in a 'closed' state. The overall structure is fairly similar to that of a voltage-gated ion channel, but there are several structural features unique to TRP channels. In the second paper, Erhu Cao et al. present the structures of rat TRPV1 in the presence of a peptide neurotoxin (resiniferatoxin) and in the presence of capsaicin, yielding structures of activated states of the channel. Comparison of the closed and open structures suggests that TRPV1 has a unique two-gate mechanism of channel activation.

Article | | Nature

AMPA-subtype ionotropic glutamate receptors (AMPARs) are ligand-gated ion channels that mediate the majority of fast excitatory chemical neurotransmission, which underlies both learning and memory. In the brain, these receptors form complexes with auxiliary proteins, which alter channel kinetics and receptor pharmacology, and many neurological diseases are linked to AMPAR signalling. However, an activated AMPAR structure has been difficult to obtain and the understanding of channel gating and signal transduction is limited. Here, Alexander Sobolevsky and colleagues report the structures of AMPAR complexes with auxiliary proteins by cryo-electron microscopy, providing the first view of an activated AMPAR. This work provides the basis for gating and the conformational and permeation pathway changes associated with the receptor cycle of activation, desensitization, and recovery from desensitization for ionotropic glutamate receptors.

Article | | Nature

This study describes the use of electron cryomicroscopy to determine structures of three of the main rotational states of a eukaryotic V-ATPase, providing the first insight into the conformational changes that occur during rotary catalysis. V-ATPases are rotary enzymes which use the energy released by ATP hydrolysis to pump protons across a lipid bilayer, thereby controlling the pH of many intracellular compartments. The three structures, of the enzyme from the yeast Saccharomyces cerevisiae, reveal several large conformational changes that explain how rotation in the soluble, catalytic region of this ATPase is coupled to the membrane-bound, proton-translocating region. The structures also reveal that two long, highly tilted transmembrane α-helices in the a-subunit interact with the c-ring.

Letter | | Nature

Shee-Mei Lok and colleagues provide a 3.7 Å cryo-electron microscopy view of Zika virus, revealing typical flavivirus architecture. They report that in contrast to the related flavivirus dengue virus, Zika virus is thermally stable at 40 °C, and speculate that this structural stability may contribute to the ability of the virus to survive in semen, saliva and urine.

Letter | | Nature

Mechanosensation forms the basis of many of our senses, including touch, balance, hearing and pain. Mechanically gated ion channels are responsible for transmitting mechanical force into electrical signals. However, how this occurs is not well understood at the molecular level. Here the authors report the structure of the Drosophila mechanotransduction channel NOMPC by single-particle cryo-electron microscopy. The channel contains a long, helical domain of ankyrin repeats, which appears to undergo a spring-like motion. This motion allows the mechanical movement of the cytoskeleton to be relayed into opening the channel.

Letter | | Nature

During protein synthesis, transfer RNAs move sequentially through the A, P and E sites of the ribosome as their attached amino acids are transferred to the growing peptide chain. Large conformational movements accompany their translocation. Holger Stark and colleagues have processed a staggering 1.9 million single-particle electron cryomicroscopy images of the ribosome to visualize these dynamic changes. They conclude that the conformational changes are thermally driven (or 'Brownian') and that they cause directed movement of transfer RNAs on a narrow path through the ribosome.

Article | | Nature

From the Laureates

Muscle contraction is regulated by the concentration of calcium ions in the cytoplasm of muscle cells. Ryanodine receptors (RyR) release Ca2+ from the sarcoplasmic reticulum to induce muscle contraction. Dysfunction of these channels contributes to the pathophysiology of important human diseases including muscular dystrophy. Three papers in this issue of Nature report high-resolution electron cryomicroscopy structures of the 2.2 MDa ryanodine receptor RyR1. Efremov et al. report the structure of rabbit RyR1 at 8.5 Å resolution the presence of Ca2+ in a 'partly open' state, and at 6.1 Å resolution in the absence of Ca2+ in a closed state. Zalk et al. report the rabbit RyR1 structure at 4.8 Å in the absence of Ca2+ in a closed state. And third, Yan et al. report the structure of rabbit RyR1 bound to its modulator FKBP12 at a near-atomic resolution of 3.8 Å. These papers reveal how calcium binding to the EF-hand domain of RyR1 regulates channel opening and facilitates calcium-induced calcium release. The authors also note that disease-causing mutations are clustered in regions of the channel that appear to be critical for normal channel function.

Article | | Nature

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.

Article | | Nature Structural & Molecular Biology

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.

Article | | Nature Structural & Molecular Biology

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.

News Feature | | Nature Methods

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.

Technology Feature | | Nature

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.

Commentary | Open Access | | Nature Structural & Molecular Biology

Transient receptor potential (TRP) channels are sensors for a wide range of physical and chemical stimuli. In the first of a pair of related papers, Maofu Liao et al. solve the high-resolution electron cryo-microscopy structure of rat TRPV1, the receptor for capsaicin (a pungent agent from chili peppers), in a 'closed' state. The overall structure is fairly similar to that of a voltage-gated ion channel, but there are several structural features unique to TRP channels. In the second paper, Erhu Cao et al. present the structures of rat TRPV1 in the presence of a peptide neurotoxin (resiniferatoxin) and in the presence of capsaicin, yielding structures of activated states of the channel. Comparison of the closed and open structures suggests that TRPV1 has a unique two-gate mechanism of channel activation.

News & Views | | Nature

The use of cryo-electron microscopy (cryo-EM) in structural biology has exploded in recent years as it provides structural information at near atomic resolution without the need for crystallization. However, cryo-EM has typically been limited to proteins larger than 200 kDa because of issues with low contrast. Patrick Sexton and colleagues report the structure of the full-length calcitonin receptor in complex with its peptide ligand and Gαsβγ protein by Volta phase-plate single-particle cryo-EM. This is the first G-protein-coupled receptor (GPCR) structure to be solved at high resolution by cryo-EM, the first full-length class B GPCR reported and only the second in complex with the full heterotrimeric G protein. The structure shows the GPCR in the active state and reveals key information about the conformational changes associated with peptide agonist binding and G-protein coupling in class B receptors.

News & Views | | Nature

Research, Methods and Protocols

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.

Article | | Nature Methods

Transient receptor potential (TRP) channels are sensors for a wide range of physical and chemical stimuli. In the first of a pair of related papers, Maofu Liao et al. solve the high-resolution electron cryo-microscopy structure of rat TRPV1, the receptor for capsaicin (a pungent agent from chili peppers), in a 'closed' state. The overall structure is fairly similar to that of a voltage-gated ion channel, but there are several structural features unique to TRP channels. In the second paper, Erhu Cao et al. present the structures of rat TRPV1 in the presence of a peptide neurotoxin (resiniferatoxin) and in the presence of capsaicin, yielding structures of activated states of the channel. Comparison of the closed and open structures suggests that TRPV1 has a unique two-gate mechanism of channel activation.

Article | | Nature

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.

Commentary | | Nature Methods

Following up on their 5.9 Å cryo-electron microscopy structure published less than a year ago, Kiyoshi Nagai and colleagues have now achieved a resolution of 3.7 Å for the yeast U4/U6.U5 tri-snRNP, a complex involved in splicing of messenger RNA. The improved resolution 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.

Article | | Nature

Tudor domain proteins — containing a characteristic repeated structure that recognizes methylated arginine residues — mediate various protein–protein interactions, and Tudor domains are also employed as motifs to recognize different types of histone methylation marks. 53BP1, a protein involved early in the DNA damage response that determines the pathway of repair, has tandem Tudor domains. Daniel Durocher and colleagues have determined the cryo-electron microscopy structure of a 53BP1 dimer bound to a nucleosome core particle containing two types of histone modifications: a methyl group and a ubiquitin moiety. The structure illustrates how dual recognition of both marks as well as elements on the histones themselves mediates highly specified recognition and recruitment of 53BP1.

Letter | | Nature

The conversion of light into usable energy within a photosynthesizing cell occurs within the light-harvesting complex (LHC) and photosystem (PS) complex. To understand this process, it is critical to know how excitation energy is transferred from the peripheral LHC antenna to the core PS structure. Zhenfeng Liu and colleagues have determined a high-resolution structure of a 1.1-MDa plant PSII–LHCII supercomplex by single-particle cryo-electron microscopy. They find that each monomer of the homodimeric supercomplex contains 25 proteins and 133 pigment cofactors. Some differences are seen compared to cyanobacterial PSII structures, but, most importantly, the ability to examine the PSII–LHCII interface permits solid predictions regarding the excitation-energy-transfer pathway.

Article | | Nature

The initiation of gene transcription in eukaryotes is tightly controlled at the promoter of each gene through the actions of the pre-initiation complex (PIC), a large multi-subunit composed of general transcription factors, and RNA polymerase II (Pol II) assembles at the promoter to ensure correct loading of Pol II and opening of the duplex DNA for transcription into RNA. Two papers published in this issue report detailed cryo-electron microscopy structures of the Pol II machinery at near-atomic resolution. Eva Nogales and colleagues present structural models of the human PIC at all major steps during transcription initiation at near-atomic resolution. They provide new mechanistic insights into the processes of promoter melting and transcription bubble stabilization, as well as proposing an almost complete structural model of all of the PIC components bound to duplex DNA. Patrick Cramer and colleagues report structures of yeast initiation complexes containing all of the basal transcription factors except TFIIH, and containing either closed or open promoter DNA. They show that DNA opening can occur in the absence of TFIIH, and provide mechanistic insights into DNA opening and template-strand loading. The structures reveal the high structural conservation between yeast and human transcription initiation systems.

Article | | Nature

The initiation of gene transcription in eukaryotes is tightly controlled at the promoter of each gene through the actions of the pre-initiation complex (PIC), a large multi-subunit composed of general transcription factors, and RNA polymerase II (Pol II) assembles at the promoter to ensure correct loading of Pol II and opening of the duplex DNA for transcription into RNA. Two papers published in this issue report detailed cryo-electron microscopy structures of the Pol II machinery at near-atomic resolution. Eva Nogales and colleagues present structural models of the human PIC at all major steps during transcription initiation at near-atomic resolution. They provide new mechanistic insights into the processes of promoter melting and transcription bubble stabilization, as well as proposing an almost complete structural model of all of the PIC components bound to duplex DNA. Patrick Cramer and colleagues report structures of yeast initiation complexes containing all of the basal transcription factors except TFIIH, and containing either closed or open promoter DNA. They show that DNA opening can occur in the absence of TFIIH, and provide mechanistic insights into DNA opening and template-strand loading. The structures reveal the high structural conservation between yeast and human transcription initiation systems.

Article | | Nature

The use of cryo-electron microscopy (cryo-EM) in structural biology has exploded in recent years as it provides structural information at near atomic resolution without the need for crystallization. However, cryo-EM has typically been limited to proteins larger than 200 kDa because of issues with low contrast. Patrick Sexton and colleagues report the structure of the full-length calcitonin receptor in complex with its peptide ligand and Gαsβγ protein by Volta phase-plate single-particle cryo-EM. This is the first G-protein-coupled receptor (GPCR) structure to be solved at high resolution by cryo-EM, the first full-length class B GPCR reported and only the second in complex with the full heterotrimeric G protein. The structure shows the GPCR in the active state and reveals key information about the conformational changes associated with peptide agonist binding and G-protein coupling in class B receptors.

Article | | Nature

Alzheimer's disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. The lesions are made of paired helical and straight tau filaments (PHFs and SFs, respectively). Different tau filaments characterize other neurodegenerative diseases, suggesting that molecular conformers of aggregated tau underlie human tauopathies. No high-resolution structures of tau filaments are currently available. Here, Sjors Scheres and colleagues present cryo-electron microscopy (cryo-EM) maps at 3.5 Å resolution and corresponding atomic models of PHFs and SFs from the brain of an individual with Alzheimer's disease. Their results show that cryo-EM enables atomic characterization of amyloid filaments from patient-derived material and could be used to study a range of neurodegenerative diseases.

Article | | Nature

The human γ-secretase complex, comprising presenilin 1 (PS1), PEN-2, APH-1, and nicastrin, is a membrane-embedded protease that controls a number of important cellular functions through substrate cleavage. Dysfunction of the enzyme is thought to cause Alzheimer's disease. This paper reports the first atomic structure of an intact human γ-secretase complex, determined at 3.4 Å resolution by cryo-electron microscopy. The structure illustrates how a remarkably plastic active site is positioned inside the membrane through specific interactions of four components of γ-secretase. Alzheimer's disease-derived mutations affect residues that cluster at two hotspots, each located at the center of a distinct four-transmembrane segment bundle in PS1.

Article | | Nature

In a variety of cellular processes — including neurotransmitter release, hormone release and vesicle trafficking — the evolutionarily conserved SNARE proteins form a complex that drives fusion between membranes of two cellular compartments. Once fusion occurs, these complexes are disassembled by the ATPase enzyme NSF and the SNAP adaptor proteins to recycle individual SNAREs for another round of membrane fusion. This study reports the use of single-particle electron cryomicroscopy to determine sub-nanometre to near-atomic resolution structures of NSF and the 20S complex. This paper reports the structures of full-length NSF in ATP- and ADP-bound states, and those of the roughly 660-kilodalton NSF/SNAP/SNARE (20S) super-complex involving two different SNARE complexes. The authors' data provide unprecedented details of the inner-workings of these essential molecular machines.

Article | | Nature

Filamentous actin (F-actin) — a main component of the cytoskeleton — is the major protein of thin filaments in the muscle. The binding of the motor protein myosin to F-actin is mediated by another protein called tropomyosin, which also binds to F-actin in smooth muscle and in non-muscle cells, stabilizing and regulating these filaments. Using electron cryomicroscopy, Stefan Raunser and colleagues have obtained the first high-resolution, three-dimensional structure of F-actin in complex with tropomyosin. The structure reveals the interactions that stabilize the F-actin and sheds light on the possible effect of prominent disease-causing mutations. Comparison of the F-actin structure with the crystal structure of monomeric (G)-actin reveals conformational changes associated with filament formation.

Letter | | Nature

Bacteriophage T4 uses its contractile tail to inject its genome into a bacterial host cell. Central to this process is the baseplate, at the end of the tail. In a tour-de-force of structural biology, Nicholas Taylor, Petr Leiman and colleagues use cryo-electron microscopy to create an atomic model of the T4 baseplate in its pre- and post-host attachment conformations providing the first molecular view of the sequence of events that leads to the transition between these two states. The baseplate–tail tube complex comprises 145 polypeptide chains of 15 different proteins, and the structures reveal how the baseplate couples host recognition to sheath contraction. The structure and organization of all core baseplate components are conserved in a range of bacterial contractile devices, suggesting that their baseplates employ a similar mechanism for triggering sheath contraction.

Article | | Nature

Mitochondrial electron transport chain complexes are responsible for cellular respiration and energy production. They are organized in supercomplexes called respirasomes. Two studies in this issue of Nature report cryo-electron microscopy structures of the supercomplex consisting of complex I, the dimer of complex III and complex IV at resolutions ranging from 5.4 Å to 7.8 Å. Maojun Yang and colleagues study the respirasome isolated from porcine heart, whereas Leonid Sazanov and colleagues obtain it from ovine heart. The structures provide insights into the organization of subunits within complexes and the interactions between the complexes.

Article | | Nature

Muscle contraction is regulated by the concentration of calcium ions in the cytoplasm of muscle cells. Ryanodine receptors (RyR) release Ca2+ from the sarcoplasmic reticulum to induce muscle contraction. Dysfunction of these channels contributes to the pathophysiology of important human diseases including muscular dystrophy. Three papers in this issue of Nature report high-resolution electron cryomicroscopy structures of the 2.2 MDa ryanodine receptor RyR1. Efremov et al. report the structure of rabbit RyR1 at 8.5 Å resolution the presence of Ca2+ in a 'partly open' state, and at 6.1 Å resolution in the absence of Ca2+ in a closed state. Zalk et al. report the rabbit RyR1 structure at 4.8 Å in the absence of Ca2+ in a closed state. And third, Yan et al. report the structure of rabbit RyR1 bound to its modulator FKBP12 at a near-atomic resolution of 3.8 Å. These papers reveal how calcium binding to the EF-hand domain of RyR1 regulates channel opening and facilitates calcium-induced calcium release. The authors also note that disease-causing mutations are clustered in regions of the channel that appear to be critical for normal channel function.

Article | | Nature

Muscle contraction is regulated by the concentration of calcium ions in the cytoplasm of muscle cells. Ryanodine receptors (RyR) release Ca2+ from the sarcoplasmic reticulum to induce muscle contraction. Dysfunction of these channels contributes to the pathophysiology of important human diseases including muscular dystrophy. Three papers in this issue of Nature report high-resolution electron cryomicroscopy structures of the 2.2 MDa ryanodine receptor RyR1. Efremov et al. report the structure of rabbit RyR1 at 8.5 Å resolution the presence of Ca2+ in a 'partly open' state, and at 6.1 Å resolution in the absence of Ca2+ in a closed state. Zalk et al. report the rabbit RyR1 structure at 4.8 Å in the absence of Ca2+ in a closed state. And third, Yan et al. report the structure of rabbit RyR1 bound to its modulator FKBP12 at a near-atomic resolution of 3.8 Å. These papers reveal how calcium binding to the EF-hand domain of RyR1 regulates channel opening and facilitates calcium-induced calcium release. The authors also note that disease-causing mutations are clustered in regions of the channel that appear to be critical for normal channel function.

Article | | Nature