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- PDB-8gt3: Crystal structure of human cardiac alpha actin P109A mutant (ADP-... -

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Basic information

Entry
Database: PDB / ID: 8gt3
TitleCrystal structure of human cardiac alpha actin P109A mutant (ADP-Pi state) in complex with fragmin F1 domain
Components
  • Actin, alpha cardiac muscle 1
  • Actin-binding protein fragmin P
KeywordsCONTRACTILE PROTEIN / actin dynamics / ATP hydrolysis / mutagenesis / MD simulation
Function / homology
Function and homology information


actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / actin polymerization or depolymerization / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / RHOB GTPase cycle ...actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / actin polymerization or depolymerization / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / RHOB GTPase cycle / microfilament motor activity / heart contraction / myosin binding / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / sarcomere / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / lamellipodium / actin cytoskeleton / cell body / blood microparticle / hydrolase activity / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / extracellular space / extracellular exosome / ATP binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Actin, alpha cardiac muscle 1 / Actin-binding protein fragmin P
Similarity search - Component
Biological speciesHomo sapiens (human)
Physarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsIwasa, M. / Oda, T. / Takeda, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K17708 Japan
Japan Society for the Promotion of Science (JSPS)17K07373 Japan
Japan Society for the Promotion of Science (JSPS)20K06522 Japan
Japan Society for the Promotion of Science (JSPS)22K0617 Japan
CitationJournal: Front Cell Dev Biol / Year: 2023
Title: Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis.
Authors: Iwasa, M. / Takeda, S. / Narita, A. / Maeda, Y. / Oda, T.
History
DepositionSep 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,93713
Polymers61,8722
Non-polymers1,06511
Water13,709761
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-65 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.171, 91.108, 115.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 43618.527 Da / Num. of mol.: 1 / Mutation: P109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTC1, ACTC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68032
#2: Protein Actin-binding protein fragmin P


Mass: 18253.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 6 types, 772 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Disodium Hydrogenphosphate, HEPES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.5→45.55 Å / Num. obs: 96061 / % possible obs: 99.6 % / Redundancy: 6.792 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Χ2: 0.855 / Net I/σ(I): 15.8 / Num. measured all: 652435
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.596.2640.9771.879539415412152300.6621.06298.8
1.59-1.76.4990.6522.989359214472144000.820.70799.5
1.7-1.846.6760.414.869016513552135060.9330.44399.7
1.84-2.026.8760.2219.078552012468124370.9810.23899.8
2.02-2.257.0880.12815.828034511341113350.9930.13899.9
2.25-2.67.0830.08423.157105910036100320.9970.09100
2.6-3.187.0820.05332.5260590855685550.9980.057100
3.18-4.497.2890.03152.9848736668666860.9990.033100
4.49-45.556.9680.02757.8527034388938800.9990.02999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
MOLREP11.6.03phasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W50

7w50


Resolution: 1.5→45.55 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 4871 5.07 %
Rwork0.1646 91187 -
obs0.1662 96058 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.49 Å2 / Biso mean: 19.933 Å2 / Biso min: 8.11 Å2
Refinement stepCycle: final / Resolution: 1.5→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 61 792 4910
Biso mean--21.57 32.47 -
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.31851540.27852953310798
1.52-1.540.29391710.24132985315699
1.54-1.560.26581550.23282966312199
1.56-1.580.24611700.223530233193100
1.58-1.60.23951690.22012939310898
1.6-1.620.25741590.214329973156100
1.62-1.640.27571390.22083010314999
1.64-1.670.26111770.221730013178100
1.67-1.690.25971710.21743016318799
1.69-1.720.22591640.199230083172100
1.72-1.750.21281570.19542991314899
1.75-1.780.23421670.193430253192100
1.78-1.820.21871630.179129833146100
1.82-1.850.19711650.177430373202100
1.85-1.890.21781550.168930403195100
1.89-1.940.20451500.162830153165100
1.94-1.990.2131620.167930483210100
1.99-2.040.21710.173730153186100
2.04-2.10.20691270.166630713198100
2.1-2.170.17941660.147630443210100
2.17-2.240.17051630.149930453208100
2.24-2.330.19761600.154630543214100
2.33-2.440.19071570.154530523209100
2.44-2.570.20431570.156530883245100
2.57-2.730.17731630.157130743237100
2.73-2.940.18891730.162130663239100
2.94-3.240.19391610.155130953256100
3.24-3.70.17481610.138831183279100
3.7-4.670.13911680.128931543322100
4.67-45.550.19161960.168732743470100

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