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Yorodumi- PDB-4pki: Complex of ATP-actin With the C-terminal Actin-Binding Domain of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pki | ||||||
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Title | Complex of ATP-actin With the C-terminal Actin-Binding Domain of Tropomodulin | ||||||
Components |
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Keywords | Contractile Protein/Actin-Binding Protein / Tmod / Actin Filament / Pointed-End Capping Protein / Tropomyosin / Contractile Protein / Actin-binding Protein / Contractile Protein-Actin-Binding Protein complex | ||||||
Function / homology | Function and homology information pointed-end actin filament capping / lens fiber cell development / myofibril assembly / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cardiac muscle cell contraction / cell projection assembly / Striated Muscle Contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cytoskeletal motor activator activity / cortical actin cytoskeleton / phagocytosis, engulfment / cortical cytoskeleton / myofibril / tropomyosin binding / mesenchyme migration / hepatocyte apoptotic process / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / sarcoplasm / actin monomer binding / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / stress fiber / titin binding / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / sarcomere / adult locomotory behavior / filopodium / central nervous system development / muscle contraction / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / cytoskeleton / blood microparticle / hydrolase activity / Amyloid fiber formation / protein domain specific binding / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rao, J.N. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2014 Title: Actin cytoskeleton. Mechanism of actin filament pointed-end capping by tropomodulin. Authors: Rao, J.N. / Madasu, Y. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pki.cif.gz | 413.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pki.ent.gz | 337.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pki_validation.pdf.gz | 746.7 KB | Display | wwPDB validaton report |
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Full document | 4pki_full_validation.pdf.gz | 754.8 KB | Display | |
Data in XML | 4pki_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 4pki_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/4pki ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pki | HTTPS FTP |
-Related structure data
Related structure data | 4pkgC 4pkhC 1io0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle / References: UniProt: P68135 | ||
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#2: Protein | Mass: 36042.801 Da / Num. of mol.: 1 Fragment: Gelsolin (UNP residues 12-136), GGSGGSGGS linker, Tmod1 Actin-binding site 2 (UNP residues 160-349) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSN, TMOD1, D9S57E, TMOD / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06396, UniProt: P28289 | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.25 M sodium chloride, 12% w/v PEG3350 / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2013 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45 Å / Num. obs: 43679 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IO0 Resolution: 2.3→45 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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