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- PDB-4cfr: Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with no... -
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Basic information
Entry | Database: PDB / ID: 4cfr | |||||||||
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Title | Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA | |||||||||
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![]() | CA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / CA-BINDING / EF-HAND | |||||||||
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 / actomyosin contractile ring / regulated exocytosis / uropod / blood vessel endothelial cell migration / actin filament-based movement / RAGE receptor binding / meiotic spindle organization / actomyosin / lysosome localization / plasma membrane repair / myosin filament / myoblast fusion / RHO GTPases Activate ROCKs / actomyosin structure organization / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / myosin II complex / 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 / microfilament motor activity / leukocyte migration / phagocytosis, engulfment / EPHA-mediated growth cone collapse / chemoattractant activity / endodermal cell differentiation / cell leading edge / RHO GTPases activate PAKs / cytoskeletal motor activity / brush border / monocyte differentiation / cleavage furrow / membrane protein ectodomain proteolysis / transition metal ion binding / immunological synapse / epithelial to mesenchymal transition / stress fiber / protein-membrane adaptor activity / RHO GTPases activate PKNs / ruffle / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / 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 / actin cytoskeleton / integrin binding / protein transport / actin binding / regulation of cell shape / actin cytoskeleton organization / angiogenesis / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Duelli, A. / Kiss, B. / Lundholm, I. / Bodor, A. / Radnai, L. / Petoukhov, M. / Svergun, D. / Nyitray, L. / Katona, G. | |||||||||
![]() | ![]() Title: The C-Terminal Random Coil Region Tunes the Ca2+-Binding Affinity of S100A4 Through Conformational Activation. Authors: Duelli, A. / Kiss, B. / Lundholm, I. / Bodor, A. / Radnai, L. / Petoukhov, M. / Svergun, D. / Nyitray, L. / Katona, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.8 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cfqC ![]() 3zwhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12018.653 Da / Num. of mol.: 2 / Fragment: RESDIUES 1-101 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 5358.213 Da / Num. of mol.: 1 / Fragment: RESIDUES 1893-1935 / Mutation: YES 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: 2.42 Å3/Da / Density % sol: 49.31 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 0.2 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 11, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29.1 Å / Num. obs: 57504 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZWH Resolution: 1.4→29.09 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 15.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.229 Å2 / ksol: 0.407 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.09 Å
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Refine LS restraints |
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LS refinement shell |
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