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- EMDB-44154: The structure of human cardiac F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-44154
TitleThe structure of human cardiac F-actin
Map dataFinal map used for model building. Post process and sharpening done in phenix using density modification scheme.
Sample
  • Complex: Human cardiac F-actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsactin / cardiac / human / sarcomere / CONTRACTILE PROTEIN
Function / homology
Function and homology information


actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / I band / RHOB GTPase cycle / microfilament motor activity ...actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / I band / RHOB GTPase cycle / microfilament motor activity / heart contraction / myosin binding / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / cardiac muscle contraction / actin filament organization / sarcomere / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / actin cytoskeleton / cell body / response to ethanol / blood microparticle / hydrolase activity / response to xenobiotic stimulus / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / extracellular space / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDoran MH / Sousa D / Rynkiewicz MJ / Lehman W / Cammarato A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R56HL124091-01 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL036153-33 United States
CitationJournal: iScience / Year: 2025
Title: The hypertrophic cardiomyopathy-associated A331P actin variant enhances basal contractile activity and elicits resting muscle dysfunction.
Authors: Matthew H Doran / Michael J Rynkiewicz / Evan Despond / Meera C Viswanathan / Aditi Madan / Kripa Chitre / Axel J Fenwick / Duncan Sousa / William Lehman / John F Dawson / Anthony Cammarato /
Abstract: Previous studies aimed at defining the mechanistic basis of hypertrophic cardiomyopathy caused by A331P cardiac actin have reported conflicting results. The mutation is located along an actin surface ...Previous studies aimed at defining the mechanistic basis of hypertrophic cardiomyopathy caused by A331P cardiac actin have reported conflicting results. The mutation is located along an actin surface strand, proximal to residues that interact with tropomyosin. These F-actin-tropomyosin associations are vital for proper contractile inhibition. To help resolve disease pathogenesis, we implemented a multidisciplinary approach. Transgenic , expressing A331P actin, displayed skeletal muscle hypercontraction and elevated basal myocardial activity. A331P thin filaments, reconstituted using recombinant human cardiac actin, exhibited higher myosin-based sliding speeds, exclusively at low Ca concentrations. Cryo-EM-based reconstructions revealed no detectable A331P-related structural perturbations in F-actin. , however, the P331-containing actin surface strand was less mobile and established diminished van der Waal's attractive forces with tropomyosin, which correlated with greater variability in inhibitory tropomyosin positioning. Such mutation-induced effects potentially elevate resting contractile activity among our models and may stimulate pathology in patients.
History
DepositionMar 20, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44154.png

Downloads & links

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Map

FileDownload / File: emd_44154.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map used for model building. Post process and sharpening done in phenix using density modification scheme.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 95 pix.
= 100.51 Å		1.06 Å/pix.
x 101 pix.
= 106.858 Å		1.06 Å/pix.
x 175 pix.
= 185.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.4308176 - 2.2998092
Average (Standard dev.)0.000000000006664 (±0.20214956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin905392
Dimensions10117595
Spacing95101175
CellA: 100.509995 Å / B: 106.857994 Å / C: 185.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Post-processed map in RELION.

Fileemd_44154_additional_1.map
AnnotationPost-processed map in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refinement from RELION without post-processing.

Fileemd_44154_additional_2.map
AnnotationRefinement from RELION without post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_44154_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_44154_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human cardiac F-actin

EntireName: Human cardiac F-actin
Components
  • Complex: Human cardiac F-actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human cardiac F-actin

SupramoleculeName: Human cardiac F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: ACTC was expressed in Sf21 insect cells, using recombinant baculoviruses, and purified via gelsolin affinity chromatography
Source (natural)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf21
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / 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: Homo sapiens (human)
Molecular weightTheoretical: 42.07791 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVLSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Details: 2 mmolL-1 Tris (pH 8), 0.2 mmolL-1 CaCl2, 0.2 mmolL-1 ATP, 0.5 mmolL-1 b-mercaptoethanol, 0.002% NaN3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.93 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.48 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133289
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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