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- PDB-2n2n: Tom1 negatively modulates binding of Tollip to phosphatidylinosit... -

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Basic information

Entry
Database: PDB / ID: 2n2n
TitleTom1 negatively modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism
ComponentsTarget of Myb protein 1
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / azurophil granule membrane / endosomal transport / clathrin binding ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / azurophil granule membrane / endosomal transport / clathrin binding / polyubiquitin modification-dependent protein binding / specific granule membrane / ubiquitin binding / endocytosis / protein transport / early endosome membrane / early endosome / endosome membrane / endosome / Neutrophil degranulation / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Target of Myb protein 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...Target of Myb protein 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / ENTH/VHS / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Target of Myb1 membrane trafficking protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model detailsscore result from Rosetta, 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 11, 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

Downloads & links

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Assembly

Deposited unit
A: Target of Myb protein 1


Theoretical massNumber of molelcules
Total (without water)11,5011
Polymers11,5011
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 / 7500all calculated structures submitted
RepresentativeModel #1score result from rosetta

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Components

#1: Protein Target of Myb protein 1 / VPG


Mass: 11501.086 Da / Num. of mol.: 1 / Fragment: GAT domain residues 215-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOM1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60784

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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 HCACO
1513D HN(CA)CB
1813D 1H-15N NOESY
1913D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.8-1.0 mM [U-99% 13C; U-99% 15N] Tom1 GAT, 1.0-1.2 mM Tollip TBD, 50 uM DSS, 50 mM potassium chloride, 20 mM [U-2H] TRIS, 1 mM sodium azide, 1 mM [U-2H] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTom1 GAT-1[U-99% 13C; U-99% 15N]0.8-1.01
mMTollip TBD-21.0-1.21
50 uMDSS-31
50 mMpotassium chloride-41
20 mMTRIS-5[U-2H]1
1 mMsodium azide-61
1 mMDTT-7[U-2H]1
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
Bruker AvanceBrukerAVANCE6001
Varian Agilent DD2VarianAgilent DD29002

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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
TopSpinBruker Biospincollection
RosettaShen, Vernon, Baker and Baxrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: DGSA-DISTANCE GEOMETRY SIMULATED ANNEALING
NMR representativeSelection criteria: score result from rosetta
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 7500 / Conformers submitted total number: 20

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