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- PDB-2rtx: Solution structure of the GGQ domain of YaeJ protein from Escheri... -

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Basic information

Entry
Database: PDB / ID: 2rtx
TitleSolution structure of the GGQ domain of YaeJ protein from Escherichia coli
ComponentsPeptidyl-tRNA hydrolase YaeJ
KeywordsHYDROLASE / GGC domain
Function / homology
Function and homology information


translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / rescue of stalled ribosome / ribosome binding / cytoplasm
Similarity search - Function
Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase ArfB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / restrained energy minimization
Model detailsclosest to the average, model5
AuthorsNameki, N. / Enomoto, M. / Kogure, H. / Tochio, N. / Guntert, P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ
Authors: Kogure, H. / Handa, Y. / Nagata, M. / Kanai, N. / Guntert, P. / Kubota, K. / Nameki, N.
History
DepositionSep 21, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: 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: Peptidyl-tRNA hydrolase YaeJ


Theoretical massNumber of molelcules
Total (without water)13,4731
Polymers13,4731
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Peptidyl-tRNA hydrolase YaeJ / PTH / Alternative ribosome-rescue factor B


Mass: 13473.391 Da / Num. of mol.: 1 / Fragment: UNP residues 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yaeJ, b0191, JW0187 / Production host: Escherichia coli (E. coli) / References: UniProt: P40711, peptidyl-tRNA hydrolase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-13C; U-15N]GGQ domain-1, 20mM [U-2H]TRIS-2, 100mM NaCl-3, 1mM [U-2H]DTT-4, 0.02% NaN3-5, 10% [U-2H]H2O-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGGQ domain-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
100 mMNaCl-31
1 mMDTT-4[U-2H]1
0.02 %NaN3-51
10 %H2O-6[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.93Guntert et al.structure solution
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OPALp1.4Koradi, Guntert, Billeterrefinement
KUJIRAKobayashi, N.data analysis
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: restrained energy minimization / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 5

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