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Yorodumi- PDB-4z94: Actin Complex With a Chimera of Tropomodulin-1 and Leiomodin-1 Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z94 | ||||||
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Title | Actin Complex With a Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 | ||||||
Components |
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Keywords | PROTEIN BINDING/STRUCTURAL PROTEIN / Actin Nucleator / ATP-actin / PROTEIN BINDING-STRUCTURAL PROTEIN complex | ||||||
Function / homology | Function and homology information pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / 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 ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / 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 / positive regulation of actin filament polymerization / 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 / Smooth Muscle Contraction / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rebowski, G. / Boczkowska, M. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: How Leiomodin and Tropomodulin use a common fold for different actin assembly functions. Authors: Boczkowska, M. / Rebowski, G. / Kremneva, E. / Lappalainen, P. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z94.cif.gz | 399.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z94.ent.gz | 326 KB | Display | PDB format |
PDBx/mmJSON format | 4z94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z94_validation.pdf.gz | 811.4 KB | Display | wwPDB validaton report |
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Full document | 4z94_full_validation.pdf.gz | 824.3 KB | Display | |
Data in XML | 4z94_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 4z94_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/4z94 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z94 | HTTPS FTP |
-Related structure data
Related structure data | 4z79C 4z8gC 4pkiS 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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1 |
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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) / References: UniProt: P68135 | ||
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#2: Protein | Mass: 36533.457 Da / Num. of mol.: 1 Fragment: Gelsolin residues 12-136 (UNP), linker,Tropomodulin-1 residues 160-228 (UNP), Leiomodin-1 Actin-Binding Site 2 (UNP residues 364-486) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSN, TMOD1, D9S57E, TMOD, LMOD1 / Production host: Escherichia coli (E. coli) References: UniProt: P06396, UniProt: P28289, UniProt: P29536 | ||
#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: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 20% PEG3350, 200 mM lithium sulfate, 100 mM Tris, pH 8.8, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Feb 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.9 Å / Num. all: 27926 / Num. obs: 27914 / % possible obs: 89.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.92 / % possible all: 50.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PKI Resolution: 2.4→39.812 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.24 / 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: 2.4→39.812 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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