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- PDB-1e8b: Solution structure of 6F11F22F2, a compact three-module fragment ... -

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Basic information

Entry
Database: PDB / ID: 1e8b
TitleSolution structure of 6F11F22F2, a compact three-module fragment of the gelatin-binding domain of human fibronectin
ComponentsFIBRONECTIN
KeywordsCELL ADHESION / EXTRACELLULAR MATRIX GLYCOPROTEIN
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 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 / AB INITIO SIMULATED ANNEALING
Model type detailsMINIMIZED AVERAGE
AuthorsPickford, A.R. / Smith, S.P. / Staunton, D. / Boyd, J. / Campbell, I.D.
CitationJournal: Embo J. / Year: 2001
Title: The Hairpin Structure of the (6)F1(1)F2(2)F2 Fragment from Human Fibronectin Enhances Gelatin Binding
Authors: Pickford, A.R. / Smith, S.P. / Staunton, D. / Boyd, J. / Campbell, I.D.
History
DepositionSep 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Non-polymer description / Other ...Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Nov 28, 2012Group: Database references / Derived calculations
Revision 1.3Feb 14, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nmr_software / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_mr / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRONECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0932
Polymers17,8721
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein FIBRONECTIN / / FN / COLD-INSOLUBLE GLOBULIN / CIG /


Mass: 17871.625 Da / Num. of mol.: 1 / Fragment: 6F11F22F2, RESIDUES 305-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: EXTRACELLULARGlossary of biology / Plasmid: PPIC9K / Cellular location (production host): SECRETED / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P02751
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D [1H-1H] NOESY (60MS MIXIMG TIME)
1213D [1H-15N] NOESY (60MS MIXING TIME)
131HMQC-J.
NMR detailsText: THE STRUCTURE WAS DETERMINED BY HETERONUCLEAR NMR SPECTROSCOPY ON UNIFORMLY 15N-LABELED 6F11F22F2.

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Sample preparation

DetailsContents: 2MM 6F11F22F2, 20MM PHOSPHATE BUFFER
Sample conditionspH: 4.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: HOME BUILT SPECTROMETER INCORPORATING OXFORD INSTRUMENTS MAGNET
Manufacturer: Oxford / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.9BRUNGER ET AL.refinement
Felix2.3structure solution
NMRViewstructure solution
CNSstructure solution
RefinementMethod: AB INITIO SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers submitted total number: 1

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