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Yorodumi- PDB-2rkz: Crystal structure of the second and third fibronectin f1 modules ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rkz | |||||||||
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Title | Crystal structure of the second and third fibronectin f1 modules in complex with a fragment of staphylococcus aureus fnbpa-1 | |||||||||
Components |
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Keywords | CELL ADHESION / fibrronectin / 2F13F1 / beta zipper / staphylococcus aureus / Acute phase / Alternative splicing / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphorylation / Pyrrolidone carboxylic acid / Secreted / Sulfation / Cell wall / Peptidoglycan-anchor / Virulence | |||||||||
Function / homology | Function and homology information aggregation of unicellular organisms / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex ...aggregation of unicellular organisms / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / fibrinogen binding / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / fibronectin binding / Signaling by ALK fusions and activated point mutants / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / cell-matrix adhesion / Integrin signaling / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / heparin binding / nervous system development / heart development / regulation of cell shape / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Bingham, R.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains Authors: Bingham, R.J. / Meenan, N.A. / Schwarz-Linek, U. / Turkenburg, J.P. / Garman, E.F. / Potts, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rkz.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rkz.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rkz ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rkz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 10120.389 Da / Num. of mol.: 6 / Fragment: UNP residues 93-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FN1 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P02751 #2: Protein/peptide | Mass: 2459.572 Da / Num. of mol.: 6 / Fragment: UNP residues 529-549 / Source method: obtained synthetically / Details: Peptide synthesis Source: (synth.) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: P14738 #3: Chemical | #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: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.8M SUCCINIC ACID, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2006 Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2→26.038 Å / Num. all: 61539 / Num. obs: 58424 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.2 / Num. measured all: 33090 / Num. unique all: 8970 / Rsym value: 0.272 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A previous lower resolution structure Resolution: 2→25.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.723 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 24.358 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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