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Yorodumi- PDB-2fn2: SOLUTION NMR STRUCTURE OF THE GLYCOSYLATED SECOND TYPE TWO MODULE... -
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-Basic information
Entry | Database: PDB / ID: 2fn2 | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE GLYCOSYLATED SECOND TYPE TWO MODULE OF FIBRONECTIN, 20 STRUCTURES | ||||||
Components | FIBRONECTIN | ||||||
Keywords | GLYCOPROTEIN / FIBRONECTIN / TYPE TWO MODULE / GLYCOSYLATED PROTEIN / COLLAGEN | ||||||
Function / homology | Function and homology information 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 ...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 / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / 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) / 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 / GPER1 signaling / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heparin binding / heart development / nervous system development / regulation of cell shape / protease binding / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / blood microparticle / 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) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS | ||||||
Authors | Sticht, H. / Pickford, A.R. / Potts, J.R. / Campbell, I.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Solution structure of the glycosylated second type 2 module of fibronectin. Authors: Sticht, H. / Pickford, A.R. / Potts, J.R. / Campbell, I.D. #1: Journal: Structure / Year: 1997 Title: Solution Structure of a Type 2 Module from Fibronectin: Implications for the Structure and Function of the Gelatin-Binding Domain Authors: Pickford, A.R. / Potts, J.R. / Bright, J.R. / Phan, I. / Campbell, I.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fn2.cif.gz | 361.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fn2.ent.gz | 298.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fn2_validation.pdf.gz | 382.8 KB | Display | wwPDB validaton report |
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Full document | 2fn2_full_validation.pdf.gz | 515.6 KB | Display | |
Data in XML | 2fn2_validation.xml.gz | 30 KB | Display | |
Data in CIF | 2fn2_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fn2 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fn2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6703.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 375 - 433 Source method: isolated from a genetically manipulated source Details: GLYCOSYLATED SECOND TYPE II MODULE / Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULAR / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 (HIS4-) / References: UniProt: P02751 |
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#2: Sugar | ChemComp-NAG / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: TWO-DIMENSIONAL 1H-1H |
-Sample preparation
Details | Contents: H2O/D2O(9:1) OR D2O |
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Sample conditions | Ionic strength: 0 mM / pH: 4.5 / Pressure: 10E+5 PA atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Home-built OMEGA 500 / Manufacturer: Home-built / Model: OMEGA 500 / Field strength: 500 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA Conformers calculated total number: 80 / Conformers submitted total number: 20 |