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- PDB-1t1h: NMR solution structure of the U box domain from AtPUB14, an armad... -

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Basic information

Entry
Database: PDB / ID: 1t1h
TitleNMR solution structure of the U box domain from AtPUB14, an armadillo repeat containing protein from Arabidopsis thaliana
Componentsarmadillo repeat containing protein
KeywordsLIGASE / UBIQUITIN LIGASE / E3 LIGASE / ARABIDOPSIS / U-BOX
Function / homology
Function and homology information


transmembrane receptor protein serine/threonine kinase binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nucleus / cytoplasm
Similarity search - Function
U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
U-box domain-containing protein 14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsAndersen, P. / Kragelund, B.B. / Olsen, A.N. / Larsen, F.H. / Chua, N.-H. / Poulsen, F.M. / Skriver, K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and Biochemical Function of a Prototypical Arabidopsis U-box Domain
Authors: Andersen, P. / Kragelund, B.B. / Olsen, A.N. / Larsen, F.H. / Chua, N.-H. / Poulsen, F.M. / Skriver, K.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: armadillo repeat containing protein


Theoretical massNumber of molelcules
Total (without water)8,7631
Polymers8,7631
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 / 200structures with favorable non-bond energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein armadillo repeat containing protein / GSPEF-ATPUB14


Mass: 8762.994 Da / Num. of mol.: 1 / Fragment: U-box domain (249-321)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VZ40

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC, HN(CA)CB,CBCA(CO)NH, HNCO
122HN(CA)CO
1333D 15N-separated TOCSY, 3D 15N-separated NOESY
1443D 13C-separated TOCSY
1553D 13C-separated TOCSY, 3D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM GSPEF-AtPUB14(249-321) U-15N,13C, 20 mM sodium phosphate, 0.15 M NaCl, 1 mM DTT, 10% D2010% D20, 90% H20
20.6 mM GSPEF-AtPUB14(249-321) U-15N,13C, 20 mM sodium phosphate, 0.15 M NaCl, 1 mM DTT, 10% D2010% D20, 90% H20
30.6 mM GSPEF-AtPUB14(249-321) U-15N, 20 mM sodium phosphate, 0.15 M NaCl, 1 mM DTT, 10% D2010% D20, 90% H20
40.4 mM GSPEF-AtPUB14(249-321) U-15N,13C, 20 mM sodium phosphate, 0.15 M NaCl, 1 mM DTT, 99.96% D2099.96% D20, 0.04% H2O
50.5 mM GSPEF-AtPUB14(249-321) U-15N,13C, 20 mM sodium phosphate, 0.15 M NaCl, 1 mM DTT, 99.96% D2099.96% D20, 0.04% H2O
Sample conditionsIonic strength: 20 mM sodium phosphate, 0.15M NaCl / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA7501
Varian UNITY INOVAVarianUNITY INOVA8002

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
Pronto20020517data analysis
CYANAstructure solution
X-PLORV3.840structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1083 NOE-derived distance constraints and 88 dihedral angle contraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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