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Yorodumi- PDB-4cfr: Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with no... -
+Open data
-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 | |||||||||
Components |
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Keywords | CA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / CA-BINDING / EF-HAND | |||||||||
Function / homology | Function and homology information 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 / actomyosin contractile ring ...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 / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / regulated exocytosis / uropod / blood vessel endothelial cell migration / actin filament-based movement / meiotic spindle organization / RAGE receptor binding / actomyosin / lysosome localization / myosin filament / plasma membrane repair / myoblast fusion / actomyosin structure organization / myosin II complex / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / CD163 mediating an anti-inflammatory response / microfilament motor activity / platelet formation / phagocytosis, engulfment / leukocyte migration / EPHA-mediated growth cone collapse / endodermal cell differentiation / chemoattractant activity / cell leading edge / RHO GTPases activate PAKs / brush border / monocyte differentiation / cleavage furrow / cytoskeletal motor activity / membrane protein ectodomain proteolysis / transition metal ion binding / immunological synapse / Signaling by ALK fusions and activated point mutants / epithelial to mesenchymal transition / protein-membrane adaptor activity / stress fiber / RHO GTPases activate PKNs / ruffle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / integrin-mediated signaling pathway / ADP binding / FCGR3A-mediated phagocytosis / adherens junction / neuromuscular junction / cytoplasmic side of plasma membrane / spindle / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / calcium-dependent protein binding / protein transport / actin filament binding / actin cytoskeleton / integrin binding / actin binding / regulation of cell shape / actin cytoskeleton organization / collagen-containing extracellular matrix / angiogenesis / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Duelli, A. / Kiss, B. / Lundholm, I. / Bodor, A. / Radnai, L. / Petoukhov, M. / Svergun, D. / Nyitray, L. / Katona, G. | |||||||||
Citation | Journal: Plos One / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cfr.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfr.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfr ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfr | HTTPS FTP |
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-Related structure data
Related structure data | 4cfqC 3zwhS 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 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.) HOMO SAPIENS (human) / Cell line: HEK / Plasmid: PBH4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26447 #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.) HOMO SAPIENS (human) / Cell line: HEK / Plasmid: PBH4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35579 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0722 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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