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- PDB-2lgt: Backbone 1H, 13C, and 15N Chemical Shift Assignments for QFM(Y)F -

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Basic information

Entry
Database: PDB / ID: 2lgt
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for QFM(Y)F
ComponentsEukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION
Function / homology
Function and homology information


translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosome binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWong, L.E. / Li, Y. / Pillay, S. / Pervushin, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1
Authors: Wong, L.E. / Li, Y. / Pillay, S. / Frolova, L. / Pervushin, K.
History
DepositionAug 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: 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 / database_2 / 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_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: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)16,0801
Polymers16,0801
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic peptide chain release factor subunit 1 / Eukaryotic release factor 1 / eRF1 / Protein Cl1 / TB3-1


Mass: 16079.643 Da / Num. of mol.: 1 / Fragment: UNP residues 1-142 / Mutation: T122Q, S123F, L124M, L126F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62495

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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 HNCA
1313D HN(CA)CB
1413D HNCO
1513D 1H-15N NOESY
1613D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.1mM DSS-1, 100mM potassium chloride-2, 20mM MES-3, 5% [U-2H] D2O-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMDSS-11
100 mMpotassium chloride-21
20 mMMES-31
5 %D2O-4[U-2H]1
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / 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
NameDeveloperClassification
CARAKeller and Wuthrichdata analysis
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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