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- PDB-2n1k: Structure of the Third Type III Domain from Human Fibronectin -

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Basic information

Entry
Database: PDB / ID: 2n1k
TitleStructure of the Third Type III Domain from Human Fibronectin
ComponentsFibronectin
KeywordsSTRUCTURAL PROTEIN / FN3 domain / fibronectin / extracellular matrix protein
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / endothelial cell migration / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / positive regulation of fibroblast proliferation / 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 / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / GPER1 signaling / Platelet degranulation / nervous system development / heparin binding / regulation of cell shape / heart development / protease binding / : / Interleukin-4 and Interleukin-13 signaling / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / 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 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 / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsStine, J.M. / Sun, Y. / Armstrong, G. / Briknarova, K.
CitationJournal: Biochemistry / Year: 2015
Title: Structure and Unfolding of the Third Type III Domain from Human Fibronectin.
Authors: Stine, J.M. / Sun, Y. / Armstrong, G. / Bowler, B.E. / Briknarova, K.
History
DepositionApr 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin


Theoretical massNumber of molelcules
Total (without water)11,3371
Polymers11,3371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11337.204 Da / Num. of mol.: 1 / Fragment: third FN3 domain (UNP residues 808-905)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: P02751
Sequence detailsT16P (UNP T817P) IS A NATURAL VARIANT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HN(CA)CO
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D HBCB(CGCD)HD
11523D 1H-15N NOESY
11622D 15N HMQC
11732D DQF-COSY
11832D 1H-1H TOCSY
11932D 1H-1H NOESY
12042D DQF-COSY
12142D 1H-1H TOCSY
12242D 1H-1H NOESY
12352D 13C/15N-filtered 13C/15N-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-99% 13C; U-99% 15N] 3FN3, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-99% 15N] 3FN3, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM 3FN3, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.6 mM 3FN3, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 100% D2O100% D2O
50.9 mM [U-99% 13C; U-99% 15N] 3FN3, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 0.9 mM 3FN3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mM3FN3-1[U-99% 13C; U-99% 15N]1
10 mMsodium phosphate-21
1.8 mMpotassium phosphate-31
140 mMsodium chloride-41
2.7 mMpotassium chloride-51
0.6 mM3FN3-6[U-99% 15N]2
10 mMsodium phosphate-72
1.8 mMpotassium phosphate-82
140 mMsodium chloride-92
2.7 mMpotassium chloride-102
0.6 mM3FN3-113
10 mMsodium phosphate-123
1.8 mMpotassium phosphate-133
140 mMsodium chloride-143
2.7 mMpotassium chloride-153
0.6 mM3FN3-164
10 mMsodium phosphate-174
1.8 mMpotassium phosphate-184
140 mMsodium chloride-194
2.7 mMpotassium chloride-204
0.9 mM3FN3-21[U-99% 13C; U-99% 15N]5
10 mMsodium phosphate-225
1.8 mMpotassium phosphate-235
140 mMsodium chloride-245
2.7 mMpotassium chloride-255
0.9 mM3FN3-265
Sample conditionsIonic strength: 0.17 / pH: 7.5 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Varian NMR SystemVarianVarian NMR System6001
Varian Varian NMR SystemVarianVarian NMR System8002

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Processing

NMR software
NameDeveloperClassification
VnmrJAgilentcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmrCCPNdata analysis
CcpNmrCCPNchemical shift assignment
CcpNmrCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeneration of torsion angle restraints
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Cartesian dynamics and Powell minimization in explicit water (default Aria refinement protocol)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 25

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