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- PDB-1o7b: Refined solution structure of the human TSG-6 Link module -

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Entry
Database: PDB / ID: 1o7b
TitleRefined solution structure of the human TSG-6 Link module
ComponentsTUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6
KeywordsCELL ADHESION / HYALURONAN-BINDING DOMAIN / CARBOHYDRATE-BINDING DOMAIN / LINK MODULE / GLYCOPROTEIN
Function / homology
Function and homology information


fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / carboxylesterase activity / negative regulation of neutrophil chemotaxis / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway ...fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / carboxylesterase activity / negative regulation of neutrophil chemotaxis / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of receptor clustering / negative regulation of inflammatory response / tertiary granule lumen / cell-cell signaling / ficolin-1-rich granule lumen / cell adhesion / positive regulation of cell migration / inflammatory response / calcium ion binding / Neutrophil degranulation / signal transduction / extracellular space / extracellular region
Similarity search - Function
Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Tumor necrosis factor-inducible gene 6 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / AB INITIO SIMULATED ANNEALING
AuthorsBlundell, C.D. / Teriete, P. / Kahmann, J.D. / Pickford, A.R. / Campbell, I.D. / Day, A.J.
Citation
Journal: J. Biol. Chem. / Year: 2003
Title: The link module from ovulation- and inflammation-associated protein TSG-6 changes conformation on hyaluronan binding.
Authors: Blundell, C.D. / Mahoney, D.J. / Almond, A. / DeAngelis, P.L. / Kahmann, J.D. / Teriete, P. / Pickford, A.R. / Campbell, I.D. / Day, A.J.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: The Link Module from Human Tsg-6 Inhibits Neutrophil Migration in a Hyaluronan- and Inter-Alpha -Inhibitor-Independent Manner
Authors: Getting, S.J. / Mahoney, D.J. / Cao, T. / Rugg, M.S. / Fries, E. / Milner, C.M. / Perretti, M. / Day, A.J.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Hyaluronan Binding Properties of a Cd44 Chimera Containing the Link Module of Tsg-6
Authors: Lesley, J. / English, N.M. / Gal, I. / Mikecz, K. / Day, A.J. / Hyman, R.
#3: Journal: J.Biol.Chem. / Year: 2001
Title: Mapping the Hyaluronan-Binding Site on the Link Module from Human Tumor Necrosis Factor-Stimulated Gene-6 by Site-Directed Mutagenesis
Authors: Mahoney, D.J. / Blundell, C.D. / Day, A.J.
#4: Journal: Structure / Year: 2000
Title: Localization and Characterization of the Hyaluronan-Binding Site on the Link Module from Human Tsg-6
Authors: Kahmann, J.D. / O'Brien, R. / Werner, J.M. / Heinegard, D. / Ladbury, J.E. / Campbell, I.D. / Day, A.J.
#5: Journal: Protein Expr.Purif. / Year: 1997
Title: Method for Quantitative Refolding of the Link Module from Human Tsg-6
Authors: Kahmann, J.D. / Koruth, R. / Day, A.J.
#6: Journal: Protein Expr.Purif. / Year: 1996
Title: Overexpression, Purification, and Refolding of Link Module from Human Tsg-6 in Escherichia Coli: Effect of Temperature, Media, and Mutagenesis on Lysine Misincorporation at Arginine Aga Codons
Authors: Day, A.J. / Aplin, R.T. / Willis, A.C.
#7: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Solution Structure of the Link Module: A Hyaluronan-Binding Domain Involved in Extracellular Matrix Stability and Cell Migration
Authors: Kohda, D. / Morton, C.J. / Parkar, A.A. / Hatanaka, H. / Inagaki, F.M. / Campbell, I.D. / Day, A.J.
#8: Journal: J.Cell Biol. / Year: 1992
Title: A Novel Secretory Tumour Necrosis Factor-Inducible Protein (Tsg-6) is a Member of the Family of Hyaluronate Binding Proteins, Closely Related to the Adhesion Receptor Cd44
Authors: Lee, T.H. / Wisniewski, H.G. / Vilcek, J.
History
DepositionOct 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
SupersessionNov 7, 2003ID: 1TSG
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Structure summary / Category: pdbx_nmr_representative
Item: _pdbx_nmr_representative.conformer_id / _pdbx_nmr_representative.selection_criteria
Revision 1.4Jan 24, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _pdbx_nmr_spectrometer.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: TUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6


Theoretical massNumber of molelcules
Total (without water)10,9471
Polymers10,9471
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 / 250LEAST RESTRAINT VIOLATION
RepresentativeModel #1lowest energy

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Components

#1: Protein TUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6 / HUMAN TSG-6 / HYALURONATE-BINDING PROTEIN / TNF-STIMULATED GENE 6 PROTEIN


Mass: 10946.578 Da / Num. of mol.: 1 / Fragment: LINK_MODULE, RESIDUES 36-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: EXTRACELLULAR, INFLAMMATION-ASSOCIATED / Plasmid: PRK172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P98066
Compound detailsPOSSIBLE ROLE IN CELL-MATRIX INTERACTIONS DURING INFLAMMATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY-HSQC
12115N-HSQC-NOESY-HSQC
13113C-NOESY-HSQC
1412D-NOESY
NMR detailsText: STRUCTURE DETERMINED BY NMR SPECTROSCOPY ON UNIFORMLY 15N- AND 13C,15N-LABELLED LINK_TSG6

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Sample preparation

DetailsContents: 10% D2O, 1-3MM LINK_TSG6
Sample conditionsIonic strength: ~2MM NA IONS / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home built incorporating Oxford Instruments magnetHome-builtHOMEBUILT7501
Home built incorporating Oxford Instruments magnetHome-builtHOMEBUILT6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
FELIX2.3structure solution
XEASYstructure solution
CNSstructure solution
RefinementMethod: AB INITIO SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 250 / Conformers submitted total number: 20

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