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Yorodumi- PDB-8gt1: Crystal structure of human cardiac alpha actin A108G mutant (ADP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gt1 | |||||||||||||||
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Title | Crystal structure of human cardiac alpha actin A108G mutant (ADP-Pi state) in complex with fragmin F1 domain | |||||||||||||||
Components |
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Keywords | CONTRACTILE 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 / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / microfilament motor activity / RHOB GTPase cycle / myosin binding ...actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / microfilament motor activity / RHOB GTPase cycle / myosin binding / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / sarcomere / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / lamellipodium / cell body / blood microparticle / hydrolase activity / focal adhesion / glutamatergic synapse / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Physarum polycephalum (eukaryote) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | |||||||||||||||
Authors | Iwasa, M. / Oda, T. / Takeda, S. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gt1.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gt1.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 8gt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/8gt1 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/8gt1 | HTTPS FTP |
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-Related structure data
Related structure data | 8gsuC 8gswC 8gt2C 8gt3C 8gt4C 8gt5C 7w50S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43630.539 Da / Num. of mol.: 1 / Mutation: A108G 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 |
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#2: Protein | 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 |
-Non-polymers , 7 types, 881 molecules
#3: Chemical | ChemComp-ADP / | ||||||||
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#4: Chemical | ChemComp-ATP / | ||||||||
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Disodium Hydrogenphosphate, HEPES |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→30.23 Å / Num. obs: 130313 / % possible obs: 99.3 % / Redundancy: 6.583 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Χ2: 0.844 / Net I/σ(I): 11.68 / Num. measured all: 857912 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W50 Resolution: 1.35→30.23 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.11 Å2 / Biso mean: 19.4629 Å2 / Biso min: 6.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→30.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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