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- PDB-2fn2: SOLUTION NMR STRUCTURE OF THE GLYCOSYLATED SECOND TYPE TWO MODULE... -

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Basic information

Entry
Database: PDB / ID: 2fn2
TitleSOLUTION NMR STRUCTURE OF THE GLYCOSYLATED SECOND TYPE TWO MODULE OF FIBRONECTIN, 20 STRUCTURES
ComponentsFIBRONECTIN
KeywordsGLYCOPROTEIN / FIBRONECTIN / TYPE TWO MODULE / GLYCOSYLATED PROTEIN / COLLAGEN
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / Extracellular matrix organization / Fibronectin matrix formation / 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 / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / Extracellular matrix organization / Fibronectin matrix formation / 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 / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / response to muscle activity / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / regulation of protein phosphorylation / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / 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 BRAF and RAF1 fusions / integrin binding / GPER1 signaling / Signaling by ALK fusions and activated point mutants / Platelet degranulation / heparin binding / regulation of cell shape / heart development / nervous system development / protease binding / angiogenesis / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / 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) / Fibronectin type II domain / Fibronectin type II domain superfamily ...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) / 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 / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsSticht, H. / Pickford, A.R. / Potts, J.R. / Campbell, I.D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Solution structure of the glycosylated second type 2 module of fibronectin.
Authors: Sticht, H. / Pickford, A.R. / Potts, J.R. / Campbell, I.D.
#1: Journal: Structure / Year: 1997
Title: Solution Structure of a Type 2 Module from Fibronectin: Implications for the Structure and Function of the Gelatin-Binding Domain
Authors: Pickford, A.R. / Potts, J.R. / Bright, J.R. / Phan, I. / Campbell, I.D.
History
DepositionAug 6, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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.process_site / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)6,9252
Polymers6,7031
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: Protein FIBRONECTIN


Mass: 6703.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 375 - 433
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED SECOND TYPE II MODULE / Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULAR / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 (HIS4-) / References: UniProt: P02751
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: TWO-DIMENSIONAL 1H-1H

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Sample preparation

DetailsContents: H2O/D2O(9:1) OR D2O
Sample conditionsIonic strength: 0 mM / pH: 4.5 / Pressure: 10E+5 PA atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Home-built OMEGA 500 / Manufacturer: Home-built / Model: OMEGA 500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
Felixstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 80 / Conformers submitted total number: 20

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