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- EMDB-45563: Cryo-EM structure of myosin-1c bound to F-actin in the ADP-A state -

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Basic information

Entry
Database: EMDB / ID: EMD-45563
TitleCryo-EM structure of myosin-1c bound to F-actin in the ADP-A state
Map data
Sample
  • Complex: Complex of myosin-1c with F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin-Ic
    • Protein or peptide: Calmodulin-1
  • 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 / 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
Calmodulin-1 / Actin, alpha skeletal muscle / Unconventional myosin-Ic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Oryctolagus cuniculus (rabbit) / Mus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 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: 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 SS / Sindelar CV / Ostap ME
History
DepositionJun 27, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45563.png

Downloads & links

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Map

FileDownload / File: emd_45563.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 384 pix.
= 516.864 Å		1.35 Å/pix.
x 384 pix.
= 516.864 Å		1.35 Å/pix.
x 384 pix.
= 516.864 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.346 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.3892138 - 6.103796
Average (Standard dev.)0.001710641 (±0.059470534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 516.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45563_msk_1.map
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Half map: #1

Fileemd_45563_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_45563_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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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: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin-Ic
    • Protein or peptide: Calmodulin-1
  • 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: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 220 KDa

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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: 4 / 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: 4 / 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: 52.0 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: 28.266 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.687 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 671620
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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