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- PDB-1qgb: SOLUTION STRUCTURE OF THE N-TERMINAL F1 MODULE PAIR FROM HUMAN FI... -

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Basic information

Entry
Database: PDB / ID: 1qgb
TitleSOLUTION STRUCTURE OF THE N-TERMINAL F1 MODULE PAIR FROM HUMAN FIBRONECTIN
ComponentsPROTEIN (FIBRONECTIN)
KeywordsCELL ADHESION / FIBRONECTIN TYPE 1 MODULE PAIR
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 / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPotts, J.R. / Bright, J.R. / Bolton, D. / Pickford, A.R. / Campbell, I.D.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of the N-terminal F1 module pair from human fibronectin.
Authors: Potts, J.R. / Bright, J.R. / Bolton, D. / Pickford, A.R. / Campbell, I.D.
History
DepositionApr 21, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_details ...database_2 / pdbx_nmr_details / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_details.text / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (FIBRONECTIN)


Theoretical massNumber of molelcules
Total (without water)10,5251
Polymers10,5251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 100LOW ENERGY AND AGREEMENT WITH EXPERIMENTAL RESTRAINTS
Representative

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Components

#1: Protein PROTEIN (FIBRONECTIN)


Mass: 10524.674 Da / Num. of mol.: 1 / Fragment: N-TERMINAL F1 MODULE PAIR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
1413D-NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NMR SPECTROSCOPY ON UNIFORMLY 15N-LABELLED 1F1-2F1

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Sample preparation

DetailsType: solution / Contents: 2.2 mM [U-15N] 1F1-2F1, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.2 mM / Component: 1F1-2F1 / Isotopic labeling: [U-15N]
Sample conditionspH: 4.0 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
ManufacturerField strength (MHz)Spectrometer-ID
Oxford5001
Oxford6002
Oxford7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOW ENERGY AND AGREEMENT WITH EXPERIMENTAL RESTRAINTS
Conformers calculated total number: 100 / Conformers submitted total number: 24

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