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- PDB-2ha1: Complex of the first and second type III domains of human Fibrone... -

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Basic information

Entry
Database: PDB / ID: 2ha1
TitleComplex of the first and second type III domains of human Fibronectin in solution
ComponentsFibronectin
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / Beta sandwich / Protein-Protein complex / Rigid body docking
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 / MET activates PTK2 signaling / extracellular matrix structural constituent / 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 / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / GPER1 signaling / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Rigid body docking with torsional flexibility at the interfacial amino acid sidechains
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
DepositionJun 12, 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 1.3Mar 9, 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,1131
Polymers22,1131
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)39 / 100Structures forming a single cluster after imposing a 50% lowest energy cutoff
RepresentativeModel #1closest to the average

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Components

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


Mass: 22113.336 Da / Num. of mol.: 1
Fragment: Fibronectin first and second type III domain pair (1F3-2F3)
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
111IPAP-HSQC
123IPAP-HSQC
133Backbone chemical shift assignments

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM 1F3-2F3 U-15N, 150mM NaCl, 20mM NaPi pH 7.0, 95% H2O, 5% D2O95% H2O/5% D2O
21.0mM 1F3-2F3 U-15N, 13C, 150mM NaCl, 20mM NaPi pH 7.0, 95% H2O, 5% D2O95% H2O/5% D2O
30.6mM 1F3-2F3 U-15N, 150mM NaCl, 20mM NaPi pH 7.0, 4% Radially compressed polyacrylamide gel, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 150mM NaCl, 20mM Na2HPO3 / pH: 7.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Home-built Home build / Manufacturer: Home-built / Model: Home build / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OmegaBeta 6.0.3b2GE/Brukercollection
NMRPipe2.3 Rev2005.319.11.22Frank 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: Rigid body docking with torsional flexibility at the interfacial amino acid sidechains
Software ordinal: 1
Details: The structure was calculated by rigid body docking using ambiguous interdomain NOE-like restraints derived from chemical shift mapping of the interface and residual dipolar couplings of the ...Details: The structure was calculated by rigid body docking using ambiguous interdomain NOE-like restraints derived from chemical shift mapping of the interface and residual dipolar couplings of the complex. 7 residues from each domain were used for the ambiguous NOEs as well as 72 RDCs total. The refinement protocol was similar to that of Clore & Schwieters, JACS 125, 2902
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: Structures forming a single cluster after imposing a 50% lowest energy cutoff
Conformers calculated total number: 100 / Conformers submitted total number: 39

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