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- EMDB-45564: Cryo-EM structure of delta-NTR myosin-1c bound to F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-45564
TitleCryo-EM structure of delta-NTR myosin-1c bound to F-actin
Map dataMasked and locally filtered final map.
Sample
  • Complex: Complex of myosin-1c with F-actin
    • Protein or peptide: Unconventional myosin-Ic
    • Protein or peptide: Calmodulin-1
  • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsF-actin / myosin / myosin-1c / cellular motility / cryo-EM / actomyosin. / STRUCTURAL PROTEIN / MOTOR PROTEIN
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 / vesicle transport along actin filament / RAS processing / FCERI mediated Ca+2 mobilization / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / PKA activation / Smooth Muscle Contraction / 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 / stereocilium / Ion homeostasis / protein targeting to membrane / myosin complex / vascular endothelial growth factor signaling pathway / positive regulation of transcription by RNA polymerase III / cytoskeletal motor activator activity / regulation of bicellular tight junction assembly / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / microfilament motor activity / myosin heavy chain binding / presynaptic endocytosis / regulation of cardiac muscle cell action potential / tropomyosin binding / positive regulation of transcription by RNA polymerase I / negative regulation of ryanodine-sensitive calcium-release channel activity / troponin I binding / filamentous actin / calcineurin-mediated signaling / mesenchyme migration / actin filament bundle / brush border / microvillus / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / skeletal muscle thin filament assembly / actin monomer binding / positive regulation of protein targeting to membrane / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / lateral plasma membrane / calcium channel inhibitor activity / cellular response to interferon-beta / stress fiber / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / phagocytic vesicle / titin binding / voltage-gated potassium channel complex / actin filament polymerization / sperm midpiece / calcium channel complex / calyx of Held / cytoplasmic vesicle membrane / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / basal plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / filopodium / spindle microtubule / actin filament / phospholipid binding
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
Calmodulin-1 / Actin, alpha skeletal muscle / Unconventional myosin-Ic
Similarity search - Component
Biological speciesMus musculus (house mouse) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChavali SS / Sindelar CV / Ostap ME
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45564.png

Downloads & links

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Map

FileDownload / File: emd_45564.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked and locally filtered final map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 384 pix.
= 512.64 Å		1.34 Å/pix.
x 384 pix.
= 512.64 Å		1.34 Å/pix.
x 384 pix.
= 512.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.335 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.6760147 - 3.92612
Average (Standard dev.)0.00058657274 (±0.04031574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 512.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45564_msk_1.map
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Half map: Unmasked, unfiltered half map #2

Fileemd_45564_half_map_1.map
AnnotationUnmasked, unfiltered half map #2
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Histogram

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Half map: Unmasked, unfiltered half map #1

Fileemd_45564_half_map_2.map
AnnotationUnmasked, unfiltered half map #1
Projections & Slices
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Sample components

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Entire : Complex of myosin-1c with F-actin

EntireName: Complex of myosin-1c with F-actin
Components
  • Complex: Complex of myosin-1c with F-actin
    • Protein or peptide: Unconventional myosin-Ic
    • Protein or peptide: Calmodulin-1
  • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of myosin-1c with F-actin

SupramoleculeName: Complex of myosin-1c with F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.862613 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Unconventional myosin-Ic

MacromoleculeName: Unconventional myosin-Ic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 92.064203 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MESALTARDR VGVQDFVLLE NFTSEAAFIE NLRRRFRENL IYTYIGPVLV SVNPYRDLQI YSRQHMERYR GVSFYEVPPH LFAVADTVY RALRTERRDQ AVMISGESGA GKTEATKRLL QFYAETCPAP ERGGAVRDRL LQSNPVLEAF GNAKTLRNDN S SRFGKYMD ...String:
MESALTARDR VGVQDFVLLE NFTSEAAFIE NLRRRFRENL IYTYIGPVLV SVNPYRDLQI YSRQHMERYR GVSFYEVPPH LFAVADTVY RALRTERRDQ AVMISGESGA GKTEATKRLL QFYAETCPAP ERGGAVRDRL LQSNPVLEAF GNAKTLRNDN S SRFGKYMD VQFDFKGAPV GGHILSYLLE KSRVVHQNHG ERNFHVFYQL LEGGEEETLR RLGLERNPQS YLYLVKGQCA KV SSINDKS DWKVMRKALS VIDFTEDEVE DLLSIVASVL HLGNIHFAAD EDSNAQVTTE NQLKYLTRLL GVEGTTLREA LTH RKIIAK GEELLSPLNL EQAAYARDAL AKAVYSRTFT WLVRKINRSL ASKDAESPSW RSTTVLGLLD IYGFEVFQHN SFEQ FCINY CNEKLQQLFI ELTLKSEQEE YEAEGIAWEP VQYFNNKIIC DLVEEKFKGI ISILDEECLR PGEATDLTFL EKLED TVKP HPHFLTHKLA DQKTRKSLDR GEFRLLHYAG EVTYSVTGFL DKNNDLLFRN LKETMCSSMN PIMAQCFDKS ELSDKK RPE TVATQFKMSL LQLVEILRSK EPAYIRCIKP NDAKQPGRFD EVLIRHQVKY LGLMENLRVR RAGFAYRRKY EAFLQRY KS LCPETWPMWA GRPQDGVAVL VRHLGYKPEE YKMGRTKIFI RFPKTLFATE DSLEVRRQSL ATKIQAAWRG FHWRQKFL R VKRSAICIQS WWRGTLGRRK AAKRKWAAQT IRRLIRGFIL RHSPRCGGLN DIFEAQKIEW HEAADYKDDD DK

UniProtKB: Unconventional myosin-Ic

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Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.723365 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTA

UniProtKB: Calmodulin-1

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.758 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.078 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2548251
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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