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- PDB-4eto: Structure of S100A4 in complex with non-muscle myosin-IIA peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 4eto | ||||||
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Title | Structure of S100A4 in complex with non-muscle myosin-IIA peptide | ||||||
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![]() | METAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / EF-hand / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN | ||||||
Function / homology | ![]() negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / cortical granule exocytosis / cytokinetic process / establishment of meiotic spindle localization / myosin II filament / establishment of T cell polarity / cortical granule / positive regulation of protein processing in phagocytic vesicle ...negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / cortical granule exocytosis / cytokinetic process / establishment of meiotic spindle localization / myosin II filament / establishment of T cell polarity / cortical granule / positive regulation of protein processing in phagocytic vesicle / regulated exocytosis / uropod / actomyosin contractile ring / blood vessel endothelial cell migration / actin filament-based movement / meiotic spindle organization / RAGE receptor binding / actomyosin / lysosome localization / plasma membrane repair / myosin filament / myoblast fusion / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / CD163 mediating an anti-inflammatory response / platelet formation / myosin II complex / microfilament motor activity / phagocytosis, engulfment / leukocyte migration / EPHA-mediated growth cone collapse / cell leading edge / chemoattractant activity / endodermal cell differentiation / cytoskeletal motor activity / RHO GTPases activate PAKs / brush border / monocyte differentiation / cleavage furrow / membrane protein ectodomain proteolysis / immunological synapse / transition metal ion binding / epithelial to mesenchymal transition / stress fiber / protein-membrane adaptor activity / RHO GTPases activate PKNs / ruffle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / integrin-mediated signaling pathway / adherens junction / FCGR3A-mediated phagocytosis / neuromuscular junction / cytoplasmic side of plasma membrane / Regulation of actin dynamics for phagocytic cup formation / ADP binding / platelet aggregation / spindle / calcium-dependent protein binding / actin filament binding / Signaling by ALK fusions and activated point mutants / protein transport / actin cytoskeleton / integrin binding / actin binding / regulation of cell shape / actin cytoskeleton organization / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / in utero embryonic development / nuclear body / calmodulin binding / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN) | ||||||
![]() | ![]() Title: Structure of S100A4 with bound peptide P Authors: Ramagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 39.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 443.5 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2q91S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | dimer bound to a peptide |
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Components
#1: Protein | Mass: 10763.358 Da / Num. of mol.: 2 / Fragment: UNP residues 1-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1922.239 Da / Num. of mol.: 1 / Fragment: Coiled coil region residues 1908-1923 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→50 Å / Num. obs: 24461 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.734 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Q91 Resolution: 1.54→45.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2494 / WRfactor Rwork: 0.2093 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8274 / SU B: 1.913 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1053 / SU Rfree: 0.1066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.68 Å2 / Biso mean: 20.1365 Å2 / Biso min: 6.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→45.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20
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