CRYO-Electron Microscopy of the Acto-Myosin-ATP Complex

1990 ◽  
Vol 48 (1) ◽  
pp. 248-249
Author(s):  
John Trinickt ◽  
Howard White
Keyword(s):  
Electron Microscopy ◽  
Atp Hydrolysis ◽  
Myosin Head ◽  
Bound State ◽  
Cross Linking ◽  
Weakly Bound ◽  
Cryo Electron Microscopy ◽  
Myosin Subfragment 1 ◽  
Attached State ◽  
High Fraction

The primary force of muscle contraction is thought to involve a change in the myosin head whilst attached to actin, the energy coming from ATP hydrolysis. This change in attached state could either be a conformational change in the head or an alteration in the binding angle made with actin. A considerable amount is known about one bound state, the so-called strongly attached state, which occurs in the presence of ADP or in the absence of nucleotide. In this state, which probably corresponds to the last attached state of the force-producing cycle, the angle between the long axis myosin head and the actin filament is roughly 45°. Details of other attached states before and during power production have been difficult to obtain because, even at very high protein concentration, the complex is almost completely dissociated by ATP. Electron micrographs of the complex in the presence of ATP have therefore been obtained only after chemically cross-linking myosin subfragment-1 (S1) to actin filaments to prevent dissociation. But it is unclear then whether the variability in attachment angle observed is due merely to the cross-link acting as a hinge.We have recently found low ionic-strength conditions under which, without resorting to cross-linking, a high fraction of S1 is bound to actin during steady state ATP hydrolysis. The structure of this complex is being studied by cryo-electron microscopy of hydrated specimens. Most advantages of frozen specimens over ambient temperature methods such as negative staining have already been documented. These include improved preservation and fixation rates and the ability to observe protein directly rather than a surrounding stain envelope. In the present experiments, hydrated specimens have the additional benefit that it is feasible to use protein concentrations roughly two orders of magnitude higher than in conventional specimens, thereby reducing dissociation of weakly bound complexes.

scholarly journals Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

2019 ◽  
Author(s):  
Yan Han ◽  
Alexis A Reyes ◽  
Sara Malik ◽  
Yuan He
Keyword(s):  
Electron Microscopy ◽  
Chromatin Remodeling ◽  
Atp Hydrolysis ◽  
Protein Complexes ◽  
Gene Activation ◽  
The Body ◽  
Cellular Processes ◽  
Cryo Electron Microscopy ◽  
Chromatin Remodeling Complex ◽  
High Resolution Structure

AbstractThe multi-subunit chromatin remodeling complex SWI/SNF1–3 is highly conserved from yeast to humans and plays critical roles in various cellular processes including transcription and DNA damage repair4, 5. It uses the energy from ATP hydrolysis to remodel chromatin structure by sliding and evicting the histone octamer6–10, creating DNA regions that become accessible to other essential protein complexes. However, our mechanistic understanding of the chromatin remodeling activity is largely hindered by the lack of a high-resolution structure of any complex from this family. Here we report the first structure of SWI/SNF from the yeast S. cerevisiae bound to a nucleosome at near atomic resolution determined by cryo-electron microscopy (cryo-EM). In the structure, the Arp module is sandwiched between the ATPase and the Body module of the complex, with the Snf2 HSA domain connecting all modules. The HSA domain also extends into the Body and anchors at the opposite side of the complex. The Body contains an assembly scaffold composed of conserved subunits Snf12 (SMARCD/BAF60), Snf5 (SMARCB1/BAF47/ INI1) and an asymmetric dimer of Swi3 (SMARCC/BAF155/170). Another conserved subunit Swi1 (ARID1/BAF250) folds into an Armadillo (ARM) repeat domain that resides in the core of the SWI/SNF Body, acting as a molecular hub. In addition to the interaction between Snf2 and the nucleosome, we also observed interactions between the conserved Snf5 subunit and the histones at the acidic patch, which could serve as an anchor point during active DNA translocation. Our structure allows us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and propose a model of how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation11–13.

scholarly journals The central part of the 5.8 S rRNA is differently arranged in programmed and free human ribosomes

2005 ◽  
Vol 387 (1) ◽  
pp. 139-145 ◽  
Author(s):  
Dmitri GRAIFER ◽  
Maxim MOLOTKOV ◽  
Anna EREMINA ◽  
Aliya VEN'YAMINOVA ◽  
Marina REPKOVA ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Ribosomal Proteins ◽  
Cross Linking ◽  
Rrna Sequence ◽  
Conformational Switch ◽  
Cryo Electron Microscopy ◽  
Initiation Of Translation ◽  
The Difference ◽  
Derivative Bound ◽  
Microscopy Images

A sequence-specific modification of the human 5.8 S rRNA in isolated 60 S subunits, non-programmed 80 S ribosomes and ribosomes complexed with mRNA and tRNAs was studied with the use of a derivative of the nonaribonucleotide UCUGUGUUU bearing a perfluorophenylazide group on the C-5 atom of the 5′-terminal uridine. Part of the oligonucleotide moiety of the derivative was complementary to the 5.8 S rRNA sequence ACACA in positions 82–86 flanked by two guanines at the 5′-terminus. The target for the cross-linking was identified as nucleotide G89 on the 5.8 S RNA. In addition, several ribosomal proteins were modified by the oligonucleotide derivative bound to the 5.8 S rRNA and proteins L6 and L8 were among them. Application of these results to known cryo-electron microscopy images of eukaryotic 60 S subunits made it possible to suggest that the central part of the 5.8 S rRNA containing the sequence 82–86 and proteins L6 and L8 are located at the base of the L1 stalk of the 60 S subunit. The efficacy of cross-linking in non-programmed 80 S ribosomes was much lower than in isolated 60 S subunits and in programmed 80 S ribosomes. We suggest that the difference in the accessibilities of the central part of the 5.8 S rRNA in the programmed and non-programmed 80 S ribosomes is caused by a conformational switch that seems to be required to dissociate the 80 S ribosomes into the subunits after termination of translation to allow initiation of translation of a new template.

scholarly journals Molecular insights into the human ABCB6 transporter

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Guangyuan Song ◽  
Sensen Zhang ◽  
Mengqi Tian ◽  
Laixing Zhang ◽  
Runyu Guo ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Transmembrane Domain ◽  
Atp Hydrolysis ◽  
Toxic Metal ◽  
Bound State ◽  
Metal Resistance ◽  
Blood Group System ◽  
Cryo Electron Microscopy ◽  
Binding Pockets ◽  
Energy Dependent

AbstractABCB6 plays a crucial role in energy-dependent porphyrin transport, drug resistance, toxic metal resistance, porphyrin biosynthesis, protection against stress, and encoding a blood group system Langereis antigen. However, the mechanism underlying porphyrin transport is still unclear. Here, we determined the cryo-electron microscopy (cryo-EM) structures of nanodisc-reconstituted human ABCB6 trapped in an apo-state and an ATP-bound state at resolutions of 3.6 and 3.5 Å, respectively. Our structures reveal a unique loop in the transmembrane domain (TMD) of ABCB6, which divides the TMD into two cavities. It restrains the access of substrates in the inward-facing state and is removed by ATP-driven conformational change. No ligand cavities were observed in the nucleotide-bound state, indicating a state following substrate release but prior to ATP hydrolysis. Structural analyses and functional characterizations suggest an “ATP-switch” model and further reveal the conformational changes of the substrate-binding pockets triggered by the ATP-driven regulation.

scholarly journals Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Jun-ichi Kishikawa ◽  
Atsuko Nakanishi ◽  
Aya Furuta ◽  
Takayuki Kato ◽  
Keiichi Namba ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Atp Hydrolysis ◽  
Atomic Resolution ◽  
Converting Enzyme ◽  
Proton Conductance ◽  
Membrane Domain ◽  
Enzyme Coupling ◽  
Cryo Electron Microscopy ◽  
Flow Through ◽  
Energy Converting

V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 domain, with proton flow through the Vo membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited Vo form.

scholarly journals Structural basis for backtracking by the SARS-CoV-2 replication–transcription complex

2021 ◽  
Vol 118 (19) ◽  
pp. e2102516118
Author(s):  
Brandon Malone ◽  
James Chen ◽  
Qi Wang ◽  
Eliza Llewellyn ◽  
Young Joo Choi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Structural Basis ◽  
Nucleoside Triphosphate ◽  
Cross Linking ◽  
Rna Dependent Rna Polymerase ◽  
Present Evidence ◽  
Cryo Electron Microscopy ◽  
Dynamics Simulations ◽  
Transcription And Replication

Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA–protein cross-linking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3′ segment of the product RNA generated by backtracking extrudes through the RdRp nucleoside triphosphate (NTP) entry tunnel, that a mismatched nucleotide at the product RNA 3′ end frays and enters the NTP entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.

scholarly journals The mechanical inhibition of the isolated Vo from V-ATPase for proton conductance

2020 ◽  
Author(s):  
Jun-ichi Kishikawa ◽  
Atsuko Nakanishi ◽  
Aya Furuta ◽  
Takayuki Kato ◽  
Keiichi Namba ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Atp Hydrolysis ◽  
Atomic Resolution ◽  
Converting Enzyme ◽  
Proton Conductance ◽  
Membrane Domain ◽  
Enzyme Coupling ◽  
Cryo Electron Microscopy ◽  
Flow Through ◽  
Energy Converting

AbstractV-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 moiety, with proton flow through the Vo membrane moiety, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo of eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and the isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo adopts the auto-inhibited form and how the holo complex prevents the formation of this inhibited Vo form.One Sentence SummaryCryo-EM structures of rotary V-ATPase reveal the ON-OFF switching mechanism of H+ translocation in the Vo membrane domain.

scholarly journals The effect of nucleotide upon a specific isomerization of actomyosin subfragment 1

1988 ◽  
Vol 256 (1) ◽  
pp. 41-46 ◽  
Author(s):  
M A Geeves ◽  
T E Jeffries
Keyword(s):  
Bound States ◽  
Bound State ◽  
Second Step ◽  
Weakly Bound ◽  
Binding Model ◽  
Nucleotide Analogues ◽  
A Value ◽  
Myosin Subfragment ◽  
Myosin Subfragment 1 ◽  
Whole Muscle

The binding of actin to myosin subfragment 1 (S1) has been shown to occur as a two-step reaction [Coates, Criddle & Geeves (1985) Biochem. J. 232, 351-356]. In the first step actin is weakly bound and the second step involves the complex isomerizing to a more tightly bound state. This isomerization can be followed specifically by monitoring the fluorescence of actin that has been covalently labelled with N-(pyren-1-yl)-iodoacetamide at Cys-374 [Geeves, Jeffries & Millar (1986) Biochemistry 25, 8454-8458]. We report here that the presence of nucleotides and nucleotide analogues affects the equilibrium between the strongly bound and weakly bound states (referred to as K2). In the presence of ATP, [gamma-thio]ATP or ADP and vanadate a value of approx. less than 10(-2) was estimated for K2. In the presence of PPi or ADP a value of approx. 2.3 or 10 respectively was obtained. An increase in KCl concentration or the presence of 40% ethylene glycol was found to decrease K2 in the presence of ADP. The data presented here are consistent with the two-step binding model proposed by Geeves, Goody & Gutfreund [(1984) J. Muscle Res. Cell Motil. 5, 351-361], where it was suggested that the transition between weakly bound and strongly bound states is closely associated with the force-generating event in whole muscle.

scholarly journals Mounting, structure and autocleavage of a type VI secretion-associated Rhs polymorphic toxin

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dukas Jurėnas ◽  
Leonardo Talachia Rosa ◽  
Martial Rey ◽  
Julia Chamot-Rooke ◽  
Rémi Fronzes ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Spike Protein ◽  
Modular Organization ◽  
Cross Linking ◽  
Multidomain Proteins ◽  
Type Vi Secretion ◽  
Cryo Electron Microscopy ◽  
Dependent Growth ◽  
Contact Dependent Growth Inhibition

AbstractBacteria have evolved toxins to outcompete other bacteria or to hijack host cell pathways. One broad family of bacterial polymorphic toxins gathers multidomain proteins with a modular organization, comprising a C-terminal toxin domain fused to a N-terminal domain that adapts to the delivery apparatus. Polymorphic toxins include bacteriocins, contact-dependent growth inhibition systems, and specialized Hcp, VgrG, PAAR or Rhs Type VI secretion (T6SS) components. We recently described and characterized Tre23, a toxin domain fused to a T6SS-associated Rhs protein in Photorhabdus laumondii, Rhs1. Here, we show that Rhs1 forms a complex with the T6SS spike protein VgrG and the EagR chaperone. Using truncation derivatives and cross-linking mass spectrometry, we demonstrate that VgrG-EagR-Rhs1 complex formation requires the VgrG C-terminal β-helix and the Rhs1 N-terminal region. We then report the cryo-electron-microscopy structure of the Rhs1-EagR complex, demonstrating that the Rhs1 central region forms a β-barrel cage-like structure that encapsulates the C-terminal toxin domain, and provide evidence for processing of the Rhs1 protein through aspartyl autoproteolysis. We propose a model for Rhs1 loading on the T6SS, transport and delivery into the target cell.

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