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- PDB-6c1d: High-Resolution Cryo-EM Structures of Actin-bound Myosin States R... -

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Entry
Database: PDB / ID: 6c1d
TitleHigh-Resolution Cryo-EM Structures of Actin-bound Myosin States Reveal the Mechanism of Myosin Force Sensing
Components
  • Actin, alpha skeletal muscle
  • Calmodulin
  • Phalloidin
  • Unconventional myosin-Ib
KeywordsSTRUCTURAL PROTEIN / Mechanochemistry / Mechanobiology / Structural Biology / Cytoskeleton / Molecular Motor / Myosin-I
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels ...post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / cytoskeletal motor activator activity / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / microfilament motor activity / myosin heavy chain binding / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / tropomyosin binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / actin filament bundle / Phase 0 - rapid depolarisation / troponin I binding / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / filamentous actin / microvillus / Unblocking of NMDA receptors, glutamate binding and activation / mesenchyme migration / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / cytoskeletal motor activity / brush border / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / actin filament bundle assembly / Long-term potentiation / skeletal muscle myofibril / protein phosphatase activator activity / striated muscle thin filament / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / skeletal muscle thin filament assembly / actin monomer binding / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / presynaptic cytosol / Activation of AMPK downstream of NMDARs / skeletal muscle fiber development / stress fiber / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / trans-Golgi network membrane / VEGFR2 mediated vascular permeability / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / ATPase, substrate binding domain, subdomain 4 / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Actin; Chain A, domain 4 / IQ motif profile. / ATPase, nucleotide binding domain / Kinesin motor domain superfamily / EF-hand / Actins signature 1. / Actin, conserved site / Actins signature 2. / : / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Recoverin; domain 1 / Actin / Actin family / Actin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
phalloidin / ADENOSINE-5'-DIPHOSPHATE / Calmodulin-1 / Actin, alpha skeletal muscle / Unconventional myosin-Ib
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Rattus norvegicus (Norway rat)
unidentified (others)
Amanita phalloides (death cap)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMentes, A. / Huehn, A. / Liu, X. / Zwolak, A. / Dominguez, R. / Shuman, H. / Ostap, E.M. / Sindelar, C.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM057247 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing.
Authors: Ahmet Mentes / Andrew Huehn / Xueqi Liu / Adam Zwolak / Roberto Dominguez / Henry Shuman / E Michael Ostap / Charles V Sindelar /
Abstract: Myosins adjust their power outputs in response to mechanical loads in an isoform-dependent manner, resulting in their ability to dynamically adapt to a range of motile challenges. Here, we reveal the ...Myosins adjust their power outputs in response to mechanical loads in an isoform-dependent manner, resulting in their ability to dynamically adapt to a range of motile challenges. Here, we reveal the structural basis for force-sensing based on near-atomic resolution structures of one rigor and two ADP-bound states of myosin-IB (myo1b) bound to actin, determined by cryo-electron microscopy. The two ADP-bound states are separated by a 25° rotation of the lever. The lever of the first ADP state is rotated toward the pointed end of the actin filament and forms a previously unidentified interface with the N-terminal subdomain, which constitutes the upper half of the nucleotide-binding cleft. This pointed-end orientation of the lever blocks ADP release by preventing the N-terminal subdomain from the pivoting required to open the nucleotide binding site, thus revealing how myo1b is inhibited by mechanical loads that restrain lever rotation. The lever of the second ADP state adopts a rigor-like orientation, stabilized by class-specific elements of myo1b. We identify a role for this conformation as an intermediate in the ADP release pathway. Moreover, comparison of our structures with other myosins reveals structural diversity in the actomyosin binding site, and we reveal the high-resolution structure of actin-bound phalloidin, a potent stabilizer of filamentous actin. These results provide a framework to understand the spectrum of force-sensing capacities among the myosin superfamily.
History
DepositionJan 4, 2018Deposition site: RCSB / Processing site: RCSB
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
P: Unconventional myosin-Ib
R: Calmodulin
F: Phalloidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,69620
Polymers310,9878
Non-polymers2,70912
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20790 Å2
ΔGint-186 kcal/mol
Surface area99950 Å2

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Components

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Protein , 3 types, 7 molecules ABCDEPR

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Unconventional myosin-Ib / Myosin I alpha / MMIa / Myosin heavy chain myr 1


Mass: 84143.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q05096
#3: Protein Calmodulin


Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others) / References: UniProt: P0DP23*PLUS

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Protein/peptide , 1 types, 1 molecules F

#4: Protein/peptide Phalloidin


Type: Cyclic peptide / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amanita phalloides (death cap) / References: phalloidin

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Non-polymers , 2 types, 12 molecules

#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Complex of actin, myosin-1b, and calmodulin with ADP and phalloidin
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 11 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -167.4 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40400
Details: Resolution estimated by post-processing in RELION using a mask with soft edges that included only the central subunit.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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