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- PDB-9b3r: The structure of human cardiac F-actin -

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Basic information

Entry
Database: PDB / ID: 9b3r
TitleThe structure of human cardiac F-actin
ComponentsActin, alpha cardiac muscle 1
KeywordsCONTRACTILE PROTEIN / actin / cardiac / human / sarcomere
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
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDoran, M.H. / Sousa, D. / Rynkiewicz, M.J. / Lehman, W. / Cammarato, A.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.0May 29, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1May 14, 2025Group: Data collection / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
E: Actin, alpha cardiac muscle 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5889
Polymers126,2343
Non-polymers1,3556
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 42077.910 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTC1, ACTC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): 21
References: UniProt: P68032, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationY

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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: Human cardiac F-actin / Type: COMPLEX
Details: ACTC was expressed in Sf21 insect cells, using recombinant baculoviruses, and purified via gelsolin affinity chromatography
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: .42 MDa / Experimental value: NO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf21
Source (recombinant)Organism: unidentified baculovirus
Buffer solutionpH: 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
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 8000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.48 ° / Axial rise/subunit: 27.93 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133289 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039000
ELECTRON MICROSCOPYf_angle_d0.58812216
ELECTRON MICROSCOPYf_dihedral_angle_d4.7161254
ELECTRON MICROSCOPYf_chiral_restr0.0431356
ELECTRON MICROSCOPYf_plane_restr0.0061563

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