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- PDB-5j6z: Structure of anastellin bound to beta-strands A and B from the th... -

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Basic information

Entry
Database: PDB / ID: 5j6z
TitleStructure of anastellin bound to beta-strands A and B from the third type III domain of fibronectin
Components
  • Anastellin
  • Fibronectin
KeywordsCELL ADHESION / extracellular matrix protein
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / peptide cross-linking / integrin activation ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / peptidase activator activity / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / regulation of protein phosphorylation / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / 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 / integrin binding / 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 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 / Signaling by ALK fusions and activated point mutants / GPER1 signaling / Platelet degranulation / nervous system development / regulation of cell shape / heparin binding / : / heart development / protease binding / angiogenesis / 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 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsStine, J.M. / Briknarova, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0846132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114657 United States
CitationJournal: Biochemistry / Year: 2017
Title: The Interaction between the Third Type III Domain from Fibronectin and Anastellin Involves beta-Strand Exchange.
Authors: Stine, J.M. / Ahl, G.J.H. / Schlenker, C. / Rusnac, D.V. / Briknarova, K.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
B: Anastellin


Theoretical massNumber of molelcules
Total (without water)13,3862
Polymers13,3862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area8940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3210.421 Da / Num. of mol.: 1 / Fragment: residues 806-834
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus(DE3)-RIPL / References: UniProt: P02751
#2: Protein Anastellin / FN / Cold-insoluble globulin / CIG


Mass: 10175.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D C(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D HNCO
181isotropic13D HN(CA)CO
191isotropic13D CCH-TOCSY
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 13C/15N-filtered, 13C(aliphatic)-edited NOESY
1131isotropic12D 13C/15N-filtered, 13C(aliphatic)-selected NOESY
1141isotropic13D 13C/15N-filtered, 15N-edited NOESY
1151isotropic12D 13C,15N-filtered, 15N-selected NOESY
1162isotropic12D 1H-15N HSQC
1172isotropic12D 1H-13C HSQC aliphatic
1182isotropic12D 1H-13C HSQC aromatic
1192isotropic13D HN(CA)CB
1202isotropic13D CBCA(CO)NH
1212isotropic13D C(CO)NH
1222isotropic13D H(CCO)NH
1232isotropic13D HNCO
1242isotropic13D HN(CA)CO
1252isotropic13D CCH-TOCSY
1262isotropic13D (H)CCH-TOCSY
1272isotropic13D 1H-13C NOESY aliphatic
1282isotropic13D 1H-13C NOESY aromatic
1292isotropic12D HBCB(CGCD)HD
1302isotropic13D 13C/15N-filtered, 13C(aliphatic)-edited NOESY
1312isotropic12D 13C/15N-filtered, 13C(aliphatic)-selected NOESY
1322isotropic13D 13C/15N-filtered, 13C(aromatic)-edited NOESY
1332isotropic12D 13C/15N-filtered, 13C(aromatic)-selected NOESY
1342isotropic13D 13C/15N-filtered, 15N-edited NOESY
1352isotropic12D 13C/15N-filtered, 15N-selected NOESY
1363isotropic12D 1H-15N HSQC
1373isotropic13D 1H-15N NOESY
1383isotropic13D 1H-15N TOCSY
1393isotropic12D DQF-COSY
1403isotropic12D TOCSY
1414isotropic12D 1H-15N HSQC
1424isotropic13D 1H-15N NOESY
1434isotropic13D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-99% 13C; U-99% 15N] AB, 0.6 mM anastellin, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2O13C15N AB:anastellin90% H2O/10% D2O
solution20.6 mM AB, 0.6 mM [U-99% 13C; U-99% 15N] anastellin, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2OAB:13C15N anastellin90% H2O/10% D2O
solution30.6 mM [U-99% 15N] AB, 0.6 mM anastellin, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2O15N AB:anastellin90% H2O/10% D2O
solution40.6 mM AB, 0.6 mM [U-99% 15N] anastellin, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, 2.7 mM potassium chloride, 90% H2O/10% D2OAB:15N anastellin90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMAB[U-99% 13C; U-99% 15N]1
0.6 mManastellinnatural abundance1
10 mMsodium phosphatenatural abundance1
1.8 mMpotassium phosphatenatural abundance1
140 mMsodium chloridenatural abundance1
2.7 mMpotassium chloridenatural abundance1
0.6 mMABnatural abundance2
0.6 mManastellin[U-99% 13C; U-99% 15N]2
10 mMsodium phosphatenatural abundance2
1.8 mMpotassium phosphatenatural abundance2
140 mMsodium chloridenatural abundance2
2.7 mMpotassium chloridenatural abundance2
0.6 mMAB[U-99% 15N]3
0.6 mManastellinnatural abundance3
10 mMsodium phosphatenatural abundance3
1.8 mMpotassium phosphatenatural abundance3
140 mMsodium chloridenatural abundance3
2.7 mMpotassium chloridenatural abundance3
0.6 mMABnatural abundance4
0.6 mManastellin[U-99% 15N]4
10 mMsodium phosphatenatural abundance4
1.8 mMpotassium phosphatenatural abundance4
140 mMsodium chloridenatural abundance4
2.7 mMpotassium chloridenatural abundance4
Sample conditionsIonic strength: 166 mM / Label: standard / pH: 7.5 / Pressure: 100000 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent NMR system / Manufacturer: Agilent / Model: NMR system / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 19

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