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- PDB-9zbp: Helical Reconstruction of the Complex of Pseudo-Acetylated Human ... -

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Basic information

Entry
Database: PDB / ID: 9zbp
TitleHelical Reconstruction of the Complex of Pseudo-Acetylated Human Cardiac Actin (K326/328Q) and Tropomyosin
Components
  • Actin, alpha cardiac muscle 1
  • Tropomyosin alpha-1 chain
KeywordsMOTOR PROTEIN / Lysine acetylation / F-actin / tropomyosin / muscle / steric regulation / cryo-EM structure / motor proteins
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / regulation of muscle contraction / bleb / Formation of the dystrophin-glycoprotein complex (DGC) / ruffle organization / cardiac muscle tissue morphogenesis ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / regulation of muscle contraction / bleb / Formation of the dystrophin-glycoprotein complex (DGC) / ruffle organization / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / muscle filament sliding / I band / sarcomere organization / structural constituent of muscle / RHOB GTPase cycle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / heart contraction / myosin binding / negative regulation of vascular associated smooth muscle cell migration / regulation of heart contraction / mesenchyme migration / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle thin filament assembly / RHOA GTPase cycle / Smooth Muscle Contraction / cardiac muscle contraction / stress fiber / cytoskeletal protein binding / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of cell adhesion / actin filament organization / negative regulation of cell migration / sarcomere / cellular response to reactive oxygen species / actin filament / filopodium / wound healing / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / actin filament binding / regulation of cell shape / actin cytoskeleton / lamellipodium / actin binding / cell body / response to ethanol / blood microparticle / cytoskeleton / hydrolase activity / response to xenobiotic stimulus / protein heterodimerization activity / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / protein homodimerization activity / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Tropomyosins signature. / Tropomyosin / Tropomyosin / 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 / Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsKarpicheva, O. / 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)HL036153 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL124091 United States
CitationJournal: J Mol Cell Cardiol / Year: 2025
Title: Pseudo-acetylation of ACTC1 K326 and K328 promotes dysinhibition of reconstituted human cardiac thin filaments.
Authors: Kripa Chitre / Olga E Karpicheva / Chloe J King / Michael J Rynkiewicz / Axel J Fenwick / John F Dawson / D Brian Foster / William Lehman / Anthony Cammarato /
Abstract: Electrostatic interactions between actin residues K326 and K328 and tropomyosin bias tropomyosin to an F-actin location where it blocks myosin attachment. K326/328 acetylation neutralizes their ...Electrostatic interactions between actin residues K326 and K328 and tropomyosin bias tropomyosin to an F-actin location where it blocks myosin attachment. K326/328 acetylation neutralizes their charge, potentially disrupting thin filament-based contractile regulation. We verified acetylation of K326/328 on human cardiac actin (ACTC1) and generated recombinant K326/328Q, pseudo-acetylated ACTC1. Pseudo-acetylation reduced inhibition of myosin-driven motility of F-actin-tropomyosin and F-actin-tropomyosin-troponin at low Ca. Cryo-EM-based and computational modeling revealed that pseudo-acetylation did not alter tropomyosin positioning along F-actin but decreased local F-actin-tropomyosin interaction energy. Thus, by reducing the energetic demands required for myosin to displace tropomyosin, ACTC1 K326/328 acetylation may promote contractile activation.
History
DepositionNov 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
B: Actin, alpha cardiac muscle 1
C: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
E: Actin, alpha cardiac muscle 1
F: Actin, alpha cardiac muscle 1
M: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
O: Tropomyosin alpha-1 chain
P: Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,77322
Polymers384,06410
Non-polymers2,70912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Helical symmetry determined by cryo-EM reconstruction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 42062.789 Da / Num. of mol.: 6 / Mutation: K326Q, K328Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTC1, ACTC / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P68032, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32921.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA / Plasmid: pET-3d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P09493
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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 K326/K328Q Cardiac F-Actin Containing Mg-ADP with Tropomyosin
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
110 mM3-(N-morpholino)propanesulfonic acidC7H15NO4S1
250 mMSodium acetateCH3COONa1
33 mMMagnesium chlorideMgCl21
41 mMDithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 9 uM Mutant F-actin was mixed with 63 uM tropomyosin and incubated for 15 minutes; then 3 uL of the mixture was applied to the grid
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K
Details: Blotting was performed with a blot force of 3 and a blot time of 3 s.

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 98 K / Temperature (min): 98 K
Image recordingElectron dose: 50.69 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4950
EM imaging opticsEnergyfilter name: TFS Selectris / Phase plate: OTHER

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv4.5.3particle selectionFilaments were collected using Filament Tracer Tool
2cryoSPARCv4.5.3image acquisition
4cryoSPARCv4.5.3CTF correction
7MDFF1.9.4a53model fitting
9PHENIX2.0.5867model refinement
12cryoSPARCv4.5.3classification
13cryoSPARCv4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.53 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C3
Particle selectionNum. of particles selected: 2346242
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1327189 / Num. of class averages: 23 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 9zbl

9zbl


Accession code: 9zbl / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421966
ELECTRON MICROSCOPYf_angle_d0.57429716
ELECTRON MICROSCOPYf_dihedral_angle_d5.553054
ELECTRON MICROSCOPYf_chiral_restr0.0433294
ELECTRON MICROSCOPYf_plane_restr0.0033844

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