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- PDB-2my9: Solution structure of N-terminal domain of human TIG3 -

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Basic information

Entry
Database: PDB / ID: 2my9
TitleSolution structure of N-terminal domain of human TIG3
ComponentsRetinoic acid receptor responder protein 3
KeywordsHYDROLASE / TIG3 / H-REV107 family / NlpC/P60 / phospholipase
Function / homology
Function and homology information


positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PE / phospholipase A1 activity / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 ...positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PE / phospholipase A1 activity / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 / acyltransferase activity / lipid catabolic process / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / negative regulation of cell population proliferation / membrane / cytoplasm / cytosol
Similarity search - Function
: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phospholipase A and acyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsWei, H. / Wang, L. / Xia, B.
CitationJournal: Febs Lett. / Year: 2015
Title: Structural and functional characterization of tumor suppressors TIG3 and H-REV107.
Authors: Wei, H. / Wang, L. / Ren, X. / Yu, W. / Lin, J. / Jin, C. / Xia, B.
History
DepositionJan 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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: Retinoic acid receptor responder protein 3


Theoretical massNumber of molelcules
Total (without water)14,0511
Polymers14,0511
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Retinoic acid receptor responder protein 3 / HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoid-inducible gene 1 protein / ...HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoid-inducible gene 1 protein / Tazarotene-induced gene 3 protein


Mass: 14050.886 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARRES3, RIG1, TIG3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9UL19, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] TIG3N, 0.03% DSS, 20 mM DTT, 50 mM sodium chloride, 50 mM potassium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTIG3N-1[U-13C; U-15N]1
3 %DSS-21
20 mMDTT-31
50 mMsodium chloride-41
50 mMpotassium chloride-51
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
DYANA3Guntert, Braun and Wuthrichstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
TopSpin3Bruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3510 / NOE intraresidue total count: 1360 / NOE long range total count: 532 / NOE medium range total count: 281 / NOE sequential total count: 586 / Hydrogen bond constraints total count: 6 / Protein other angle constraints total count: 439 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 62
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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