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- PDB-5m0a: Solution structure of isolated 15th Fibronectin III domain from h... -

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Basic information

Entry
Database: PDB / ID: 5m0a
TitleSolution structure of isolated 15th Fibronectin III domain from human fibronectin
ComponentsFibronectin
KeywordsCELL ADHESION / Fibronectin III domain / beta sheet protein / inflammation / integrin binding
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 / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / 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 / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / substrate adhesion-dependent cell spreading / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / wound healing / Signaling by high-kinase activity BRAF mutants / regulation of protein phosphorylation / 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 / GPER1 signaling / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heart development / heparin binding / nervous system development / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / protease binding / 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
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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWaltho, J.P. / Cliff, M.J. / Blumson, E. / Humphries, M.
CitationJournal: To Be Published
Title: Solution structure of isolated 15th Fibronectin III domain from human fibronectin
Authors: Waltho, J.P. / Cliff, M.J. / Blumson, E. / Humphries, M.
History
DepositionOct 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)9,3441
Polymers9,3441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5370 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9344.231 Da / Num. of mol.: 1
Fragment: 15th Fibronectin III domain, UNP residues 2108-2193
Source method: isolated from a genetically manipulated source
Details: sequence numbering starts from 395. construct is actually from residue 2109 of human fibronectin
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
111isotropic13D HNCA
121isotropic13D HN(CO)CA
131isotropic13D HN(CA)CB
141isotropic13D HN(COCA)CB
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic12D 1H-15N HSQC
282isotropic32D 1H-13C HSQC aliphatic
292isotropic12D 1H-13C TROSY aromatic
1101isotropic33D 1H-15N NOESY
1111isotropic33D 1H-13C NOESY aliphatic
2122isotropic13D (H)CCH-TOCSY
1131isotropic13D 1H-15N TOCSY
2142isotropic13D 1H-13C TOCSY
2152isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution110 mM TRIS, 150 mM sodium chloride, 0.02 ug/mL TSP, 1 mM sodium azide, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 0.5 mM EDTA, 90% H2O/10% D2Onaf15a90% H2O/10% D2O
solution210 mM [U-2H] TRIS, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 150 mM sodium chloride, 1 mM sodium azide, 0.02 ug/mL TSP, 0.5 mM EDTA, 100% D2Onaf15b100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
0.00002 mg/mLTSPnatural abundance1
1 mMsodium azidenatural abundance1
0.35 mM15th Fibronectin III domain from human fibronectin[U-13C; U-15N]1
0.5 mMEDTAnatural abundance1
10 mMTRIS[U-2H]2
0.35 mM15th Fibronectin III domain from human fibronectin[U-13C; U-15N]2
150 mMsodium chloridenatural abundance2
1 mMsodium azidenatural abundance2
0.00002 mg/mLTSPnatural abundance2
0.5 mMEDTAnatural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1none161 mMh2o6.51 bar298 K
2none161 mMd2o6.5 pH*1 bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III9503at MRC Crick

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.0CCPNchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
TopSpinBruker Biospinprocessing
CcpNmr Analysis2.4.0CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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