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- PDB-8gt4: Crystal structure of human cardiac alpha actin Q137A mutant (AMPP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gt4 | |||||||||||||||
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Title | Crystal structure of human cardiac alpha actin Q137A mutant (AMPPNP state) in complex with fragmin F1 domain | |||||||||||||||
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![]() | CONTRACTILE PROTEIN / actin dynamics / ATP hydrolysis / mutagenesis / MD simulation | |||||||||||||||
Function / homology | ![]() actin-myosin filament sliding / actin filament-based movement / cardiac myofibril assembly / actin filament severing / cardiac muscle tissue morphogenesis / barbed-end actin filament capping / actin polymerization or depolymerization / actomyosin structure organization / Striated Muscle Contraction / I band ...actin-myosin filament sliding / actin filament-based movement / cardiac myofibril assembly / actin filament severing / cardiac muscle tissue morphogenesis / barbed-end actin filament capping / actin polymerization or depolymerization / actomyosin structure organization / Striated Muscle Contraction / I band / RHOB GTPase cycle / microfilament motor activity / myosin binding / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / phosphatidylinositol-4,5-bisphosphate binding / sarcomere / filopodium / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / 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 / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Iwasa, M. / Oda, T. / Takeda, S. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.3 KB | Display | ![]() |
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PDB format | ![]() | 105.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.3 KB | Display | ![]() |
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Full document | ![]() | 776.9 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 44.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gsuC ![]() 8gswC ![]() 8gt1C ![]() 8gt2C ![]() 8gt3C ![]() 8gt5C ![]() 7w50S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 43587.516 Da / Num. of mol.: 1 / Mutation: Q137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 18099.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 705 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ANP / | ||||||
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#4: Chemical | ChemComp-MG / | ||||||
#5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % 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: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 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: 1.55→49.39 Å / Num. obs: 89716 / % possible obs: 99.6 % / Redundancy: 6.686 % / Biso Wilson estimate: 18.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Χ2: 0.846 / Net I/σ(I): 12.54 / Num. measured all: 599841 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7W50 Resolution: 1.55→49.39 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65 / 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: 72.61 Å2 / Biso mean: 24.0252 Å2 / Biso min: 9.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→49.39 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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