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- PDB-2jq8: Solution structure of the Somatomedin B domain from vitronectin p... -

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Basic information

Entry
Database: PDB / ID: 2jq8
TitleSolution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris
ComponentsVitronectin
KeywordsCELL ADHESION / somatomedin B domain / vitronectin / disulfide-rich domain / PAI-1 / uPAR
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 / molecular dynamics
AuthorsGaardsvoll, H. / Hirschberg, D. / Nielbo, S. / Mayasundari, A. / Peterson, C.B. / Jansson, A. / Jorgensen, T.J.D. / Poulsen, F.M.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure of recombinant somatomedin B domain from vitronectin produced in Pichia pastoris
Authors: Kjaergaard, M. / Gardsvoll, H. / Hirschberg, D. / Nielbo, S. / Mayasundari, A. / Peterson, C.B. / Jansson, A. / Jorgensen, T.J.D. / Poulsen, F.M. / Ploug, M.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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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)6,1751
Polymers6,1751
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Vitronectin / / Serum-spreading factor / S-protein / V75


Mass: 6174.770 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P04004

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D HN(COCA)CB
1722D 1H-1H NOESY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11013D (H)CCH-TOCSY
11113D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-99% 13C; U-99% 15N] SMB, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM SMB, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSMB[U-99% 13C; U-99% 15N]1
0.7 mMSMB2
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
ProntoKj r, Andersen and Poulsenchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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