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- PDB-6hnf: Structure in solution of human fibronectin type III-domain 14 -

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Basic information

Entry
Database: PDB / ID: 6hnf
TitleStructure in solution of human fibronectin type III-domain 14
ComponentsFibronectin
KeywordsCELL ADHESION / Fibronectin type III-domain 14
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 / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / 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 / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / 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 / torsion angle dynamics
AuthorsZhong, X. / Arnolds, O. / Krenczyk, O. / Gajewski, J. / Puetz, S. / Herrmann, C. / Stoll, R.
CitationJournal: Biochemistry / Year: 2018
Title: The Structure in Solution of Fibronectin Type III Domain 14 Reveals Its Synergistic Heparin Binding Site.
Authors: Zhong, X. / Arnolds, O. / Krenczyk, O. / Gajewski, J. / Putz, S. / Herrmann, C. / Stoll, R.
History
DepositionSep 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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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)10,0971
Polymers10,0971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5520 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 4000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fibronectin / / FN / Cold-insoluble globulin / CIG


Mass: 10096.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic23D 1H-13C NOESY
131isotropic12D 1H-15N HSQC
141isotropic22D 1H-13C HSQC
151isotropic23D HNCO
161isotropic23D HNCA
171isotropic23D HN(CA)CB
181isotropic23D CBCA(CO)NH

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Sample preparation

DetailsType: solution / Contents: 1.0 mM [U-13C; U-15N] FNIII14, 90% H2O/10% D2O / Label: CN_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: FNIII14 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 162.7 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1030 mbar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
TopSpinBruker Biospinprocessing
Refinement
MethodSoftware ordinal
simulated annealing1
torsion angle dynamics2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 20

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