3D Reconstruction of Smooth Muscle A-Actinin by Cryo Electron Microscopy

2000 ◽  
Vol 6 (S2) ◽  
pp. 244-245
Author(s):  
Jun Liu ◽  
Dianne Taylor ◽  
Kenneth A. Taylor
Keyword(s):  
Electron Microscopy ◽  
Smooth Muscle ◽  
Calcium Binding ◽  
3D Structure ◽  
Unit Cell Dimension ◽  
Lipid Monolayer ◽  
Actin Binding ◽  
Cryo Electron Microscopy ◽  
Ef Hand ◽  
Polypeptide Chains

α-Actinin is an actin crosslinking protein identified in a wide variety of cells. Both muscle and nonmuscle isoforms of α-actinin have been characterized [1]. The molecule consists of two polypeptide chains that form a rod-shaped antiparallel dimer. Each polypeptide is composed of three distinct structural regions: actin-binding domain, four triple helical repeats that form a central rod, and a carboxyl terminal domain that contains two EF hand calcium-binding sites. Here we present the 3D structure of the smooth muscle α-actinin, as determined by cryo electron microscopy at 2.0 nm resolution.Two dimensional crystals of chicken gizzard α-actinin were formed on positively charged lipid monolayer [2] and preserved frozen hydrated for TEM. The crystal has a unit cell dimension of a = 26.31 nm, b = 20.37 nm, γ= 107.10°, based on internal calibration against TMV.

scholarly journals Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections

2019 ◽  
Vol 93 (7) ◽  
Author(s):  
Yuanzhu Gao ◽  
Shanshan Liu ◽  
Jiamiao Huang ◽  
Qianqian Wang ◽  
Kunpeng Li ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
3D Structure ◽  
Structural Features ◽  
Economic Losses ◽  
Scylla Paramamosain ◽  
Multiple Infections ◽  
Mud Crab ◽  
Cryo Electron Microscopy ◽  
Novel Virus ◽  
Icosahedral Capsid

ABSTRACT Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-Å resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-Å resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus. IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.

scholarly journals Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy

2015 ◽  
Vol 112 (43) ◽  
pp. 13237-13242 ◽  
Author(s):  
Lorenzo Sborgi ◽  
Francesco Ravotti ◽  
Venkata P. Dandey ◽  
Mathias S. Dick ◽  
Adam Mazur ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Nmr Spectroscopy ◽  
Specific Binding ◽  
3D Structure ◽  
High Mobility ◽  
Atomic Resolution ◽  
Receptor Protein ◽  
Filament Formation ◽  
Cryo Electron Microscopy

Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms.

scholarly journals Formation of Hirano Bodies Induced by Expression of an Actin Cross-Linking Protein with a Gain-of-Function Mutation

2003 ◽  
Vol 2 (4) ◽  
pp. 778-787 ◽  
Author(s):  
Andrew Maselli ◽  
Ruth Furukawa ◽  
Susanne A. M. Thomson ◽  
Richard C. Davis ◽  
Marcus Fechheimer
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Cellular Response ◽  
Biological Function ◽  
Point Mutations ◽  
Actin Binding ◽  
Cross Linking ◽  
Hirano Bodies ◽  
Transmission Electron ◽  
Ef Hand

ABSTRACT Hirano bodies are paracrystalline actin filament-containing structures reported to be associated with a variety of neurodegenerative diseases. However, the biological function of Hirano bodies remains poorly understood, since nearly all prior studies of these structures were done with postmortem samples of tissue. In the present study, we generated a full-length form of a Dictyostelium 34-kDa actin cross-linking protein with point mutations in the first putative EF hand, termed 34-kDa ΔEF1. The 34-kDa ΔEF1 protein binds calcium normally but has activated actin binding that is unregulated by calcium. The expression of the 34-kDa ΔEF1 protein in Dictyostelium induces the formation of Hirano bodies, as assessed by both fluorescence microscopy and transmission electron microscopy. Dictyostelium cells bearing Hirano bodies grow normally, indicating that Hirano bodies are not associated with cell death and are not deleterious to cell growth. Moreover, the expression of the 34-kDa ΔEF1 protein rescues the phenotypes of cells lacking the 34-kDa protein and cells lacking both the 34-kDa protein and α-actinin. Finally, the expression of the 34-kDa ΔEF1 protein also initiates the formation of Hirano bodies in cultured mouse fibroblasts. These results show that the failure to regulate the activity and/or affinity of an actin cross-linking protein can provide a signal for the formation of Hirano bodies. More generally, the formation of Hirano bodies is a cellular response to or a consequence of aberrant function of the actin cytoskeleton.

scholarly journals Cryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Steven Z. Chou ◽  
Thomas D. Pollard
Keyword(s):  
Electron Microscopy ◽  
Skeletal Muscle ◽  
Active Site ◽  
Actin Filaments ◽  
Actin Polymerization ◽  
Actin Binding ◽  
Muscle Actin ◽  
Hydrophobic Cavity ◽  
Cryo Electron Microscopy ◽  
Kinetics Of

AbstractSince the fluorescent reagent N-(1-pyrene)iodoacetamide was first used to label skeletal muscle actin in 1981, the pyrene-labeled actin has become the most widely employed tool to measure the kinetics of actin polymerization and the interaction between actin and actin-binding proteins. Here we report high-resolution cryo-electron microscopy structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP (3.2 Å) or ADP-phosphate (3.0 Å) in the active site. Polymerization buries pyrene in a hydrophobic cavity between subunits along the long-pitch helix with only minor differences in conformation compared with native actin filaments. These structures explain how polymerization increases the fluorescence 20-fold, how myosin and cofilin binding to filaments reduces the fluorescence, and how profilin binding to actin monomers increases the fluorescence.

scholarly journals Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State

2016 ◽  
Vol 91 (3) ◽  
Author(s):  
Mike Strauss ◽  
Lise Schotte ◽  
Krishanthi S. Karunatilaka ◽  
David J. Filman ◽  
James M. Hogle
Keyword(s):  
Electron Microscopy ◽  
Careful Analysis ◽  
Productive Infection ◽  
Altered State ◽  
Virus Structure ◽  
Cryo Electron Microscopy ◽  
A Cell ◽  
Single Domain Antibodies ◽  
A Site ◽  
Polypeptide Chains

ABSTRACT By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. IMPORTANCE When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.

scholarly journals Alpha-actinin of the chlorarchiniophyte Bigelowiella natans

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4288 ◽  
Author(s):  
Lars Backman
Keyword(s):  
Domain Structure ◽  
Calcium Binding ◽  
Actin Filaments ◽  
Actin Binding ◽  
Cross Linking ◽  
Primary Sequence ◽  
Dimer Formation ◽  
Spectrin Repeat ◽  
Actin Binding Domain ◽  
Ef Hand

The genome of the chlorarchiniophyte Bigelowiella natans codes for a protein annotated as an α-actinin-like protein. Analysis of the primary sequence indicate that this protein has the same domain structure as other α-actinins, a N-terminal actin-binding domain and a C-terminal calmodulin-like domain. These two domains are connected by a short rod domain, albeit long enough to form a single spectrin repeat. To analyse the functional properties of this protein, the full-length protein as well as the separate domains were cloned and isolated. Characerisation showed that the protein is capable of cross-linking actin filaments into dense bundles, probably due to dimer formation. Similar to human α-actinin, calcium-binding occurs to the most N-terminal EF-hand motif in the calmodulin-like C-terminal domain. The results indicate that this Bigelowiella protein is a proper α-actinin, with all common characteristics of a typical α-actinin.

Protein modeling by homology using the example of tick-borne encephalitis serine protease NS3

2020 ◽  
pp. 59-66
Author(s):  
Nikita Ilment ◽  
Ekaterina Zinina
Keyword(s):  
Electron Microscopy ◽  
Homology Modeling ◽  
Homology Modelling ◽  
Protein Structures ◽  
3D Structure ◽  
Free Software ◽  
Homologous Proteins ◽  
Cryo Electron Microscopy ◽  
Tick Borne Encephalitis ◽  
Sequences Analysis

Homology modeling is a process of obtaining a 3D structure of a protein using various algorithms based on already known structures of homologous proteins. The spatial structure of protein is required for in silico protein evaluation. 3D structures can be obtained using different methods: NMR, Xray crystallography (XRC), and cryo-electron microscopy (cryo-EM), but these methods require a lot of time and money. At the same time, the speed of nucleotide sequences analysis is increasing, thereby creating a mismatch between the number of decoded genomes and the investigated 3D protein structures that are encoded by these sequences. Also, homology modeling is the easiest and fastest way to obtain the model of the desired protein. This review describes free software for homology modelling — SWISS-MODEL and MODELLER, how to use it and how to evaluate the results.

Cryo-EM 3D Reconstruction of Skeletal Muscle α-Actinin

2000 ◽  
Vol 6 (S2) ◽  
pp. 248-249
Author(s):  
Jinghua Tang ◽  
Dianne W. Taylor ◽  
Kenneth A. Taylor
Keyword(s):  
Skeletal Muscle ◽  
3D Reconstruction ◽  
Polypeptide Chain ◽  
Erector Spinae ◽  
Lipid Monolayer ◽  
Actin Binding ◽  
Actin Binding Domain ◽  
Ef Hand ◽  
2D Crystals ◽  
Positively Charged

α-Actinin is a member of the spectrin superfamily of actin crosslinking proteins. The molecule is an antiparallel homodimer with a polypeptide chain weight of 94-103 kDa. Each chain can be divided into three domains: the N-terminal 250 amino acids forms an actin binding domain, the central domain consisting of four spectrin-like, triple-helical repeats and the Cterminal which contains two EF hand motifs (Baron et al, 1987).Two models have been proposed for the alignment of the triple helical repeats in the α-actinin structure, an aligned model (Baron et al., 1987) and a staggered model (Taylor and Taylor, 1993). In order to resolve the controversy, we proceeded with the cryo-EM 3D reconstruction from 2D crystal grown on a positively charged lipid monolayer. From rabbit erector spinae aactinin, we obtain better ordered 2D crystals from which we have calculated a 3D reconstruction to ∼15 Å resolution.

scholarly journals Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Kouta Mayanagi ◽  
Keisuke Oki ◽  
Naoyuki Miyazaki ◽  
Sonoko Ishino ◽  
Takeshi Yamagami ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Dna Polymerase ◽  
Structural Model ◽  
Contact Point ◽  
Dna Polymerases ◽  
3D Structure ◽  
Nuclear Antigen ◽  
Structural Level ◽  
Cryo Electron Microscopy ◽  
Dna Complex

Abstract Background DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3′-5′ editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM). Results Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus abyssi onto our EM map showed the 3D atomic structural model of PolD-PCNA-DNA. In addition to the canonical interaction between PCNA and PolD via PIP (PCNA-interacting protein)-box motif, we found a new contact point consisting of a glutamate residue at position 171 in a β-hairpin of PCNA, which mediates interactions with DP1 and DP2. The DNA synthesis activity of a mutant PolD with disruption of the E171-mediated PCNA interaction was not stimulated by PCNA in vitro. Conclusions Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for conversion of its activity. This hook function of the clamp molecule may be conserved in the three domains of life.

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