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- PDB-2n40: Solution structure of the link module of human tsg-6 in presence ... -

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Basic information

Entry
Database: PDB / ID: 2n40
TitleSolution structure of the link module of human tsg-6 in presence of a chondroitin 4-sulfate hexasaccharide
ComponentsTumor necrosis factor-inducible gene 6 protein
KeywordsCELL ADHESION / LINK MODULE / TSG-6 / GLYCOPROTEIN / CHONDROITIN SULFATE
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 / simulated annealing
Model detailslowest energy, model1
AuthorsPark, Y. / Prestegard, J.H.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Insight into the Multiple Glycosaminoglycan Binding Modes of the Link Module from Human TSG-6.
Authors: Park, Y. / Jowitt, T.A. / Day, A.J. / Prestegard, J.H.
History
DepositionJun 16, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.type
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_spectrometer.type
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor-inducible gene 6 protein


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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor necrosis factor-inducible gene 6 protein / Hyaluronate-binding protein / TNF-stimulated gene 6 protein / TSG-6 / Tumor necrosis factor alpha- ...Hyaluronate-binding protein / TNF-stimulated gene 6 protein / TSG-6 / Tumor necrosis factor alpha-induced protein 6 / TNF alpha-induced protein 6


Mass: 10946.578 Da / Num. of mol.: 1 / Fragment: Link module of TSG-6, UNP residues 36-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP6, TSG6 / Plasmid: pRK172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P98066

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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 CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 50 mM MES, 0.02 % NaN3, 0.5 mM [U-100% 13C; U-100% 15N] Link-TSG, 0.6 mM CHONDROITIN 4-SULFATE HEXASACCHARIDE, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMMESnatural abundance1
0.02 %NaN3natural abundance1
0.5 mMLink-TSG-6[U-100% 13C; U-100% 15N]1
0.6 mMCHONDROITIN 4-SULFATE HEXASACCHARIDEnatural abundance1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.8Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.8Schwieters, Kuszewski, Tjandra and Clorestructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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