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- PDB-1ssu: Structural and biochemical evidence for disulfide bond heterogene... -

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Basic information

Entry
Database: PDB / ID: 1ssu
TitleStructural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin B domain of human vitronectin
ComponentsVitronectin
KeywordsCELL ADHESION / somatostatin B domain / vitronectin / disulfide bonds heterogeneity
Function / homology
Function and homology information


rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway ...rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / extracellular matrix structural constituent / Syndecan interactions / polysaccharide binding / positive regulation of wound healing / positive regulation of smooth muscle cell migration / oligodendrocyte differentiation / endodermal cell differentiation / protein polymerization / basement membrane / ECM proteoglycans / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / collagen binding / extracellular matrix organization / cell-matrix adhesion / liver regeneration / Regulation of Complement cascade / Golgi lumen / positive regulation of receptor-mediated endocytosis / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / heparin binding / positive regulation of protein binding / collagen-containing extracellular matrix / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain ...Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics in DYANA, simulated annealing, energy minimization in AMBER
AuthorsKamikubo, Y. / De Guzman, R. / Kroon, G. / Curriden, S. / Neels, J.G. / Churchill, M.J. / Dawson, P. / Oldziej, S. / Jagielska, A. / Scheraga, H.A. ...Kamikubo, Y. / De Guzman, R. / Kroon, G. / Curriden, S. / Neels, J.G. / Churchill, M.J. / Dawson, P. / Oldziej, S. / Jagielska, A. / Scheraga, H.A. / Loskutoff, D.J. / Dyson, H.J.
CitationJournal: Biochemistry / Year: 2004
Title: Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin.
Authors: Kamikubo, Y. / De Guzman, R. / Kroon, G. / Curriden, S. / Neels, J.G. / Churchill, M.J. / Dawson, P. / Oldziej, S. / Jagielska, A. / Scheraga, H.A. / Loskutoff, D.J. / Dyson, H.J.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / 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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitronectin


Theoretical massNumber of molelcules
Total (without water)5,8241
Polymers5,8241
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)20 / 20020 lowest energy structures
RepresentativeModel #1lowest energy

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Components

#1: Protein Vitronectin /


Mass: 5824.493 Da / Num. of mol.: 1 / Fragment: somatomedin B domain of human vitronectin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB(DE3) / References: UniProt: P04004

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
2422D NOESY
NMR detailsText: not applicable

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Sample preparation

Details
Solution-IDContentsSolvent system
1N15-labeled protein 20 mM sodium phosphate pH 7.590% H2O/10% D2O
2unlabeled protein 20 mM sodium phosphate pH 7.590% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1180 mM 7.5 1 atm293 K
2180 mM 7.5 1 atm293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DRXBrukerDRX7502
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Peter Guntertstructure solution
Amber7D. Case, D. Pearlman et al.structure solution
NMRPipe2003DeLaglio, F.processing
NMRView4.1.3Bruce Johnsondata analysis
Amber7D. Case, D. Pearlman et al.refinement
RefinementMethod: torsion angle dynamics in DYANA, simulated annealing, energy minimization in AMBER
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 lowest energy structures / Conformers calculated total number: 200 / Conformers submitted total number: 20

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