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- PDB-1j8k: NMR STRUCTURE OF THE FIBRONECTIN EDA DOMAIN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1j8k
TitleNMR STRUCTURE OF THE FIBRONECTIN EDA DOMAIN, NMR, 20 STRUCTURES
ComponentsFIBRONECTIN
KeywordsPROTEIN BINDING / EDA / FIBRONECTIN / TYPEIII DOMAIN
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 / 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 / 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
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNiimi, T. / Osawa, M. / Yamaji, N. / Yasunaga, K. / Sakashita, H. / Mase, T. / Tanaka, A. / Fujita, S.
CitationJournal: J.Biomol.NMR / Year: 2001
Title: NMR structure of human fibronectin EDA.
Authors: Niimi, T. / Osawa, M. / Yamaji, N. / Yasunaga, K. / Sakashita, H. / Mase, T. / Tanaka, A. / Fujita, S.
History
DepositionMay 22, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRONECTIN


Theoretical massNumber of molelcules
Total (without water)10,2221
Polymers10,2221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
Representative

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Components

#1: Protein FIBRONECTIN /


Mass: 10222.121 Da / Num. of mol.: 1 / Fragment: EXTRA DOMAIN 2 (RESIDUES 1631-1724)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: THREE-DIMENSIONAL STRUCTURE IN SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, TORSION ANGLE DYNAMICS AND RESTRAINED ENERGY REFINEMENT.

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Sample preparation

DetailsContents: 2mM EDA U-15N,13C; 50mM phosphate buffer, 400mM sodium sulfate; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 400mM sodium sulfate / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1998Delaglioprocessing
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THESE STRUCTURES CONSIST OF 1289 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND HTDROGEN EXCHANGE MEASUREMENTS AND 51 TORSION ANGLE CONSTRAINTS OBTAINED FROM COUPLING CONSTANT ...Details: THESE STRUCTURES CONSIST OF 1289 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND HTDROGEN EXCHANGE MEASUREMENTS AND 51 TORSION ANGLE CONSTRAINTS OBTAINED FROM COUPLING CONSTANT AND CHEMICAL SHIFT INDEX
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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