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- PDB-9cfw: Cryo-EM structure of myosin-1c bound to F-actin in the ADP-B state -

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Basic information

Entry
Database: PDB / ID: 9cfw
TitleCryo-EM structure of myosin-1c bound to F-actin in the ADP-B state
Components
  • Actin, alpha skeletal muscle
  • Calmodulin-1
  • Unconventional myosin-Ic
KeywordsMOTOR PROTEIN / F-actin / myosin / myosin-1c / cellular motility / cryo-EM / actomyosin
Function / homology
Function and homology information


positive regulation of cellular response to insulin stimulus / stereocilium membrane / B-WICH complex positively regulates rRNA expression / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers ...positive regulation of cellular response to insulin stimulus / stereocilium membrane / B-WICH complex positively regulates rRNA expression / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Ion transport by P-type ATPases / Calcineurin activates NFAT / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / FCERI mediated Ca+2 mobilization / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / Smooth Muscle Contraction / RAF/MAP kinase cascade / PKA activation / vesicle transport along actin filament / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Stimuli-sensing channels / B-WICH complex / Ion homeostasis / stereocilium / myosin complex / protein targeting to membrane / vascular endothelial growth factor signaling pathway / positive regulation of transcription by RNA polymerase III / regulation of bicellular tight junction assembly / cytoskeletal motor activator activity / organelle localization by membrane tethering / microfilament motor activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / tropomyosin binding / myosin heavy chain binding / calcineurin-mediated signaling / troponin I binding / negative regulation of ryanodine-sensitive calcium-release channel activity / mesenchyme migration / positive regulation of transcription by RNA polymerase I / filamentous actin / actin filament bundle / brush border / microvillus / striated muscle thin filament / protein phosphatase activator activity / actin filament bundle assembly / skeletal muscle thin filament assembly / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / skeletal muscle myofibril / actin monomer binding / positive regulation of protein targeting to membrane / catalytic complex / regulation of cardiac muscle contraction / detection of calcium ion / lateral plasma membrane / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / skeletal muscle fiber development / phagocytic vesicle / titin binding / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / calyx of Held / cytoplasmic vesicle membrane / actin filament polymerization / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / basal plasma membrane / regulation of cytokinesis / filopodium / spindle microtubule / actin filament / positive regulation of receptor signaling pathway via JAK-STAT / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Similarity search - Function
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. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...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. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Calmodulin-1 / Actin, alpha skeletal muscle / Unconventional myosin-Ic
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsChavali, S.S. / Sindelar, C.V. / Ostap, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM057247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110530 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: High-resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory.
Authors: Sai Shashank Chavali / Peter J Carman / Henry Shuman / E Michael Ostap / Charles V Sindelar /
Abstract: Myosin-IC (myo1c) is a class-I myosin that supports transport and remodeling of the plasma membrane and membrane-bound vesicles. Like other members of the myosin family, its biochemical kinetics are ...Myosin-IC (myo1c) is a class-I myosin that supports transport and remodeling of the plasma membrane and membrane-bound vesicles. Like other members of the myosin family, its biochemical kinetics are altered in response to changes in mechanical loads that resist the power stroke. However, myo1c is unique in that the primary force-sensitive kinetic transition is the isomerization that follows ATP binding, not ADP release as in other slow myosins. Myo1c also powers actin gliding along curved paths, propelling actin filaments in leftward circles. To understand the origins of this unique force-sensing and motile behavior, we solved actin-bound myo1c cryo-EM structures in the presence and absence of ADP. Our structures reveal that in contrast with other myosins, the myo1c lever arm swing is skewed, partly due to a different actin interface that reorients the motor domain on actin. The structures also reveal unique nucleotide-dependent behavior of both the nucleotide pocket as well as an element called the N-terminal extension (NTE). We incorporate these observations into a model that explains why force primarily regulates ATP binding in myo1c, rather than ADP release as in other myosins. Integrating our cryo-EM data with available crystallography structures allows the modeling of full-length myo1c during force generation, supplying insights into its role in membrane remodeling. These results highlight how relatively minor sequence differences in members of the myosin superfamily can significantly alter power stroke geometry and force-sensing properties, with important implications for biological function.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
P: Unconventional myosin-Ic
R: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,15712
Polymers234,3755
Non-polymers1,7827
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 41862.613 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Unconventional myosin-Ic / Myosin I beta / MMI-beta / MMIb


Mass: 92064.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo1c / Production host: unidentified baculovirus / References: UniProt: Q9WTI7
#3: Protein Calmodulin-1


Mass: 16723.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calm1, Calm, Cam, Cam1 / Production host: unidentified baculovirus / References: UniProt: P0DP26
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of myosin-1c with F-actin / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: unidentified baculovirus
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 167.88 ° / Axial rise/subunit: 27.38 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126845 / Symmetry type: HELICAL

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