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- PDB-1vg5: Solution Structure of RSGI RUH-014, a UBA domain from Arabidopsis cDNA -

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Basic information

Entry
Database: PDB / ID: 1vg5
TitleSolution Structure of RSGI RUH-014, a UBA domain from Arabidopsis cDNA
Componentsrhomboid family protein
Keywordsstructural genomics / unknown function / UBA domain / Arabidopsis thaliana / cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / Hrd1p ubiquitin ligase ERAD-L complex / misfolded protein binding / ubiquitin-specific protease binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / : / endoplasmic reticulum unfolded protein response / serine-type endopeptidase activity
Similarity search - Function
Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 ...Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid-like protein 15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOnuki, H. / Doi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-014, a UBA domain from Arabidopsis thaliana cDNA
Authors: Onuki, H. / Doi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S.
History
DepositionApr 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rhomboid family protein


Theoretical massNumber of molelcules
Total (without water)7,3191
Polymers7,3191
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein rhomboid family protein / RSGI RUH-014


Mass: 7319.033 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell-free protein synthesis (E. coli) / Plasmid: P030224-40 / References: UniProt: Q8LB17

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.0mM UBA domain U-15N, 13C; 20mM phosphate buffer (pH 6.0), 100mM NaCl, 1mM-d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe97.027.12.56Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.8993Kobayashi, N.data analysis
CYANA1.0.8Guentert, P.structure solution
CYANA1.0.8Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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