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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 / Ca2+ pathway / FCERI mediated Ca+2 mobilization / RHO GTPases activate IQGAPs / Smooth Muscle Contraction / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / PKA activation / vesicle transport along actin filament / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / Stimuli-sensing channels / B-WICH complex / Ion homeostasis / stereocilium / myosin complex / regulation of bicellular tight junction assembly / protein targeting to membrane / vascular endothelial growth factor signaling pathway / positive regulation of transcription by RNA polymerase III / cytoskeletal motor activator activity / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / microfilament motor activity / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / autophagosome membrane docking / presynaptic endocytosis / tropomyosin binding / positive regulation of ryanodine-sensitive calcium-release channel activity / myosin heavy chain binding / negative regulation of ryanodine-sensitive calcium-release channel activity / troponin I binding / positive regulation of transcription by RNA polymerase I / mesenchyme migration / brush border / filamentous actin / protein phosphatase activator activity / actin filament bundle / : / microvillus / adenylate cyclase binding / striated muscle thin filament / skeletal muscle thin filament assembly / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein targeting to membrane / lateral plasma membrane / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / skeletal muscle fiber development / stress fiber / titin binding / phagocytic vesicle / voltage-gated potassium channel complex / sperm midpiece / catalytic complex / calyx of Held / calcium channel complex / adenylate cyclase activator activity / actin filament polymerization / 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
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: To Be Published
Title: High resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory
Authors: Chavali, S.S. / Sindelar, C.V. / Ostap, M.E.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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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