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- PDB-2n31: Tom1 negatively modulates binding of Tollip to phosphatidylinosit... -

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Basic information

Entry
Database: PDB / ID: 2n31
TitleTom1 negatively modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism
ComponentsToll interacting protein variant
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


interleukin-1, type I receptor binding / leukocyte activation / protein localization to endosome / Toll-like receptor binding / SUMO binding / positive regulation of protein sumoylation / ubiquitin conjugating enzyme binding / interleukin-1-mediated signaling pathway / extrinsic component of plasma membrane / epithelial cell differentiation ...interleukin-1, type I receptor binding / leukocyte activation / protein localization to endosome / Toll-like receptor binding / SUMO binding / positive regulation of protein sumoylation / ubiquitin conjugating enzyme binding / interleukin-1-mediated signaling pathway / extrinsic component of plasma membrane / epithelial cell differentiation / ubiquitin binding / autophagy / kinase binding / Interleukin-1 signaling / specific granule lumen / azurophil granule lumen / ubiquitin-dependent protein catabolic process / molecular adaptor activity / early endosome / nuclear body / inflammatory response / phosphorylation / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / perinuclear region of cytoplasm / signal transduction / protein-containing complex / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Toll-interacting protein, C2 domain / Toll-interacting protein, CUE domain / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / UBA-like superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Toll-interacting protein, C2 domain / Toll-interacting protein, CUE domain / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / UBA-like superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Toll interacting protein variant / Toll-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model detailslowest energy, model1
AuthorsXiao, S. / Armstrong, G. / Capelluto, D.
CitationJournal: Structure / Year: 2015
Title: Tom1 Modulates Binding of Tollip to Phosphatidylinositol 3-Phosphate via a Coupled Folding and Binding Mechanism.
Authors: Xiao, S. / Brannon, M.K. / Zhao, X. / Fread, K.I. / Ellena, J.F. / Bushweller, J.H. / Finkielstein, C.V. / Armstrong, G.S. / Capelluto, D.G.
History
DepositionMay 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll interacting protein variant


Theoretical massNumber of molelcules
Total (without water)6,1321
Polymers6,1321
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 / 500all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Toll interacting protein variant


Mass: 6131.818 Da / Num. of mol.: 1 / Fragment: residues 32-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59FB9, UniProt: Q9H0E2*PLUS

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

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Sample preparation

DetailsContents: 0.8-1.0 mM [U-99% 13C; U-99% 15N] TBD, 1.0-1.2 mM GAT, 50 uM DSS, 20 mM [U-2H] TRIS, 50 mM potassium chloride, 1 mM [U-2H] DTT, 1 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTBD-1[U-99% 13C; U-99% 15N]0.8-1.01
mMGAT-21.0-1.21
50 uMDSS-31
20 mMTRIS-4[U-2H]1
50 mMpotassium chloride-51
1 mMDTT-6[U-2H]1
1 mMsodium azide-71
Sample conditionsIonic strength: 70 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian DD2VarianDD29001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
RosettaShen, Vernon, Baker and Baxstructure solution
RosettaShen, Vernon, Baker and Baxprocessing
RosettaShen, Vernon, Baker and Baxvalidation
RosettaShen, Vernon, Baker and Baxdata analysis
RosettaShen, Vernon, Baker and Baxcollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxvalidation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxcollection
PSVSBhattacharya and Montelionestructure solution
PSVSBhattacharya and Montelioneprocessing
PSVSBhattacharya and Montelionevalidation
PSVSBhattacharya and Montelionedata analysis
PSVSBhattacharya and Montelionecollection
SparkyGoddardstructure solution
SparkyGoddardprocessing
SparkyGoddardvalidation
SparkyGoddarddata analysis
SparkyGoddardcollection
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSCornilescu, Delaglio and Baxprocessing
TALOSCornilescu, Delaglio and Baxvalidation
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxcollection
TopSpinBruker Biospinstructure solution
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinvalidation
TopSpinBruker Biospindata analysis
Shen, Vernon, Baker, BaxBruker Biospincollection
RosettaShen, Vernon, Baker and Baxrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 500 / Conformers submitted total number: 20

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