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- PDB-4cfq: Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cfq | |||||||||
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Title | Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA | |||||||||
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![]() | CA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / S100A4 PROTEINS / 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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PDBx/mmCIF format | ![]() | 251.2 KB | Display | ![]() |
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PDB format | ![]() | 206.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cfrC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10369.749 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-88 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 5358.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 1893-1937 / 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: 4.11 Å3/Da / Density % sol: 34.97 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.1 M MIB, PH 4, 25% W/V PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | 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: 1.37→31.8 Å / Num. obs: 79285 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.37→1.44 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZWH Resolution: 1.37→31.772 Å / SU ML: 0.13 / σ(F): 2 / Phase error: 18.92 / Stereochemistry target values: ML Details: CHAIN A ONLY DEFINED UNTIL RES 87, CHAIN B DEFINED UNTIL RES 84, CHAIN Q ONLY DEFINED FROM RES 1902-RES 1928. CHAIN C DEFINED FROM RES 2, CHAIN D DEFINED UNTIL RES 84 AND CHAIN R DEFINED FROM 1902-1930
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→31.772 Å
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Refine LS restraints |
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LS refinement shell |
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