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Yorodumi- PDB-4cfq: Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100... -
+Open data
-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 | |||||||||
Components |
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Keywords | CA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / S100A4 PROTEINS / 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 / actin filament-based movement / blood vessel endothelial cell migration / meiotic spindle organization / RAGE receptor binding / actomyosin / plasma membrane repair / lysosome localization / myosin filament / 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 outer hair cells of the cochlea / Sensory processing of sound by inner 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 / cleavage furrow / cytoskeletal motor activity / monocyte differentiation / brush border / membrane protein ectodomain proteolysis / transition metal ion binding / Signaling by ALK fusions and activated point mutants / 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 / 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 / actin filament binding / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 | 4cfq.cif.gz | 251.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfq.ent.gz | 206.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfq ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfq | HTTPS FTP |
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-Related structure data
Related structure data | 4cfrC 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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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.) 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.: 2 / Fragment: RESIDUES 1893-1937 / 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: 3 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0722 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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