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- PDB-1qo6: Solution structure of a pair of modules from the gelatin-binding ... -

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Basic information

Entry
Database: PDB / ID: 1qo6
TitleSolution structure of a pair of modules from the gelatin-binding domain of fibronectin
ComponentsFIBRONECTIN
KeywordsCELL ADHESION PROTEIN / FIBRONECTIN MODULE PAIR / GELATIN-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 / 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 / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / extracellular matrix / regulation of ERK1 and ERK2 cascade / 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 / Signaling by ALK fusions and activated point mutants / response to wounding / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / protease binding / 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 II, collagen-binding / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain ...Fibronectin, type II, collagen-binding / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / 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
AuthorsBocquier, A.A. / Potts, J.R. / Pickford, A.R. / Campbell, I.D.
CitationJournal: Structure / Year: 1999
Title: Solution Structure of a Pair of Modules from the Gelatin-Binding Domain of Fibronectin
Authors: Bocquier, A.A. / Potts, J.R. / Pickford, A.R. / Campbell, I.D.
History
DepositionNov 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Experimental preparation
Category: pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pressure ..._pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_spectrometer.manufacturer

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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)11,1861
Polymers11,1861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)55 / 100LOW ENERGY AND AGREEMENT WITH EXPERIMENTAL RESTRAINTS
Representative

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Components

#1: Protein FIBRONECTIN /


Mass: 11186.238 Da / Num. of mol.: 1
Fragment: FIBRONECTIN TYPE-I AND FIBRONECTIN TYPE-II MODULE PAIR FROM COLLAGEN-BINDING DOMAIN
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
141NOESY-HSQC
151TOCSY-HSQC
NMR detailsText: THE FAMILY OF STRUCTURES HAS BEEN ALIGNED USING THE C, CA, N ATOMS OF RESIDUES LEU19, LEU28, PRO59 AND TYR68 OF THE INTERMODULE INTERFACE.

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Sample preparation

Sample conditionsLabel: sample_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
ManufacturerField strength (MHz)Spectrometer-ID
Oxford6001
Oxford7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
XPLOR3.851structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: LOW ENERGY AND AGREEMENT WITH EXPERIMENTAL RESTRAINTS
Conformers calculated total number: 100 / Conformers submitted total number: 55

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