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- PDB-9b3q: The structure of the human cardiac F-actin mutant A331P -

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Basic information

Entry
Database: PDB / ID: 9b3q
TitleThe structure of the human cardiac F-actin mutant A331P
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 / filopodium / actin filament / 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: 3.6 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: To Be Published
Title: Structure of human cardiac actin
Authors: Doran, M.H. / Rynkiewicz, M.J. / Sousa, D. / Cammarato, A. / Lehman, W.
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 1.0May 29, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jun 4, 2025Group: Data collection / Structure summary
Category: em_admin / em_software ...em_admin / em_software / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)127,6669
Polymers126,3123
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: 42103.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Human cardiac actin with the mutation A331P / 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 with mutation A331P / 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: -166.45 ° / Axial rise/subunit: 27.93 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140667 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059009
ELECTRON MICROSCOPYf_angle_d0.70412231
ELECTRON MICROSCOPYf_dihedral_angle_d5.3121254
ELECTRON MICROSCOPYf_chiral_restr0.0471356
ELECTRON MICROSCOPYf_plane_restr0.0061566

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