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- PDB-2h45: Solution structure of the second type III domain of human Fibrone... -

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Basic information

Entry
Database: PDB / ID: 2h45
TitleSolution structure of the second type III domain of human Fibronectin: ensemble of 25 structures
ComponentsFibronectin
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / beta sandwich
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / positive regulation of substrate-dependent cell migration, cell attachment to substrate / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / Fibronectin matrix formation / Attachment of bacteria to epithelial cells / enteric nervous system development / integrin activation ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / positive regulation of substrate-dependent cell migration, cell attachment to substrate / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / Fibronectin matrix formation / Attachment of bacteria to epithelial cells / enteric nervous system development / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / proteoglycan binding / MET activates PTK2 signaling / Molecules associated with elastic fibres / peptidase activator activity / neural crest cell migration / Syndecan interactions / extracellular matrix structural constituent / p130Cas linkage to MAPK signaling for integrins / biological process involved in interaction with symbiont / response to muscle activity / regulation of protein phosphorylation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / endodermal cell differentiation / Non-integrin membrane-ECM interactions / basement membrane / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / acute-phase response / cell-matrix adhesion / Cell surface interactions at the vascular wall / negative regulation of autophagy / Developmental Lineage of Pancreatic Ductal Cells / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / integrin binding / autophagy / 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 ALK fusions and activated point mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / nervous system development / regulation of cell shape / heparin binding / GPER1 signaling / heart development / extracellular matrix / 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 / endoplasmic reticulum lumen / receptor ligand activity / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / : / 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 / Simulated annealing in cartesian space
AuthorsVakonakis, I. / Campbell, I.D.
CitationJournal: Embo J. / Year: 2007
Title: Interdomain association in fibronectin: insight into cryptic sites and fibrillogenesis.
Authors: Vakonakis, I. / Staunton, D. / Rooney, L.M. / Campbell, I.D.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)10,2021
Polymers10,2021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 10202.056 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III 2(2F3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RP / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1334D 13C-separated NOESY
141HNHB
15415N IPAP-HSQC
163C-C long range couplings
173Methyl - carbonyl couplings
183Methyl - nitrogen couplings
193HACAHB

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5mM 2F3 U-15N, 20mM NaPi pH 7.0, 20mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
22mM 2F3 U-13C,15N, 20mM NaPi pH 7.0, 20mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
32mM 2F3 U-13C,15N, 20mM NaPi pH 7.0, 20mM NaCl, 100% D2O100% D2O
41mM 2F3 U-15N, 20mM NaPi pH 7.0, 20mM NaCl, 4% Radially compressed polyacrylamide gel, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 20mM NaCl, 20mM Na2HPO4 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built Home builtHome-builtHome built5001
Home-built Home builtHome-builtHome built6002

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Processing

NMR software
NameVersionDeveloperClassification
OmegaBeta 6.0.3b2GE/Brukercollection
NMRPipe2.3 Rev 2005.319.11.22Frank Delaglio, NIH/NIDDK,LCPprocessing
PIPP4.3.7Dan Garrett, NIH/NIDDK/LCPdata analysis
XPLOR-NIH2.12Schwieters, Kuszewski, Tjandra, Clore NIH/NIDDK/LCPstructure solution
XPLOR-NIH2.12Schwieters, Kuszewski, Tjandra, Clore NIH/NIDDK/LCPrefinement
RefinementMethod: Simulated annealing in cartesian space / Software ordinal: 1 / Details: Structures derived from 2827 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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