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- PDB-2n9d: Structure analysis of the Tom1 GAT domain reveals distinct ligand... -

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Basic information

Entry
Database: PDB / ID: 2n9d
TitleStructure analysis of the Tom1 GAT domain reveals distinct ligand-specific conformational states
ComponentsTarget of Myb protein 1
KeywordsTRANSPORT PROTEIN / Tom1 / early endosomes / alternative ESCRT-0 member / cargo
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / phosphatidylinositol-5-phosphate binding / autophagosome-lysosome fusion / positive regulation of autophagosome maturation / endosomal transport / azurophil granule membrane / clathrin binding ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / phosphatidylinositol-5-phosphate binding / autophagosome-lysosome fusion / positive regulation of autophagosome maturation / endosomal transport / azurophil granule membrane / 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 / cytosol / cytoplasm
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
AuthorsXiao, S. / Jeffrey, E.F. / Geoffrey, A.S. / Capelluto, D.G.S.
CitationJournal: Data Brief / Year: 2016
Title: Structure of the GAT domain of the endosomal adapter protein Tom1.
Authors: Xiao, S. / Ellena, J.F. / Armstrong, G.S. / Capelluto, D.G.
History
DepositionNov 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Target of Myb protein 1


Mass: 11501.086 Da / Num. of mol.: 1 / Fragment: GAT domain (UNP residues 215-309)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOM1 / Plasmid: PGEX-6P-1 / 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 HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HCACO

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Sample preparation

DetailsContents: 1.0 mM [U-99% 13C; U-99% 15N] GAT, 50 mM potassium chloride, 20 mM [U-2H] TRIS, 1 mM sodium azide, 50 uM DSS, 1 mM [U-2H] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMGAT-1[U-99% 13C; U-99% 15N]1
50 mMpotassium chloride-21
20 mMTRIS-3[U-2H]1
1 mMsodium azide-41
50 uMDSS-51
1 mMDTT-6[U-2H]1
Sample conditionsIonic strength: 70 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
SparkyGoddardprocessing
CS-ROSETTAYang, S. et al.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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