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- PDB-7r3m: Structure in solution of the TANGO1 cargo-binding domain (21-131) -

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Basic information

Entry
Database: PDB / ID: 7r3m
TitleStructure in solution of the TANGO1 cargo-binding domain (21-131)
ComponentsTransport and Golgi organization protein 1 homolog
KeywordsPROTEIN TRANSPORT / ER / TANGO1 / MIA3 / MOTH domain
Function / homology
Function and homology information


vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / cellular response to oxidised low-density lipoprotein particle stimulus / COPII-coated vesicle cargo loading / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion / endoplasmic reticulum organization / cell migration involved in sprouting angiogenesis ...vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / cellular response to oxidised low-density lipoprotein particle stimulus / COPII-coated vesicle cargo loading / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion / endoplasmic reticulum organization / cell migration involved in sprouting angiogenesis / cargo receptor activity / positive regulation of leukocyte migration / lipoprotein transport / exocytosis / endoplasmic reticulum exit site / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of cell migration / Post-translational protein phosphorylation / wound healing / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein transport / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / membrane
Similarity search - Function
Variant SH3 domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Transport and Golgi organization protein 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsArnolds, O. / Stoll, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2023
Title: Characterization of a fold in TANGO1 evolved from SH3 domains for the export of bulky cargos.
Authors: Arnolds, O. / Stoll, R.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transport and Golgi organization protein 1 homolog


Theoretical massNumber of molelcules
Total (without water)12,8901
Polymers12,8901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 6000structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Transport and Golgi organization protein 1 homolog / TANGO1 / C219-reactive peptide / D320 / Melanoma inhibitory activity protein 3


Mass: 12890.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIA3, KIAA0268, TANGO, UNQ6077/PRO20088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JRA6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N HSQC
131isotropic23D HNCO
141isotropic23D HNCA
151isotropic23D CBCA(CO)NH
161isotropic23D HN(CA)CB
171isotropic23D H(CCO)NH
181isotropic23D 1H-15N NOESY
191isotropic22D 1H-13C HSQC
1101isotropic23D (H)CCH-COSY
1111isotropic23D (H)CCH-TOCSY
1121isotropic23D 1H-13C NOESY
1131isotropic24D 13C-1H-13C HSQCNOESYHSQC
1141isotropic23D HN(CA)CO

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] TANGO1(21-131), 90% H2O/10% D2O
Label: TANGO1(21-131) / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: TANGO1(21-131) / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 25 mM HEPES, 150 mM NaCl, 1% CHAPS (w/v), 10% D2O (v/v), 0.02% (w/v) NaN3, DSS.
Ionic strength: 195 mM / Label: TANGO1(21-131) / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX600BrukerDRX6006001
Bruker AVANCE III HDBrukerAVANCE III HD7002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 6000 / Conformers submitted total number: 20

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