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- PDB-2ktu: Human eRF1 C-domain, "closed" conformer -

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Basic information

Entry
Database: PDB / ID: 2ktu
TitleHuman eRF1 C-domain, "closed" conformer
ComponentsEukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION / eRF1 / C domain / termination / Eukaryotes / Cytoplasm / Protein biosynthesis
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
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 ...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 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 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 detailsclosest to the average, model 1
AuthorsMantsyzov, A.B. / Polshakov, V.I. / Birdsall, B.
Citation
Journal: Biomol.Nmr Assign. / Year: 2007
Title: NMR assignments of the C-terminal domain of human polypeptide release factor eRF1.
Authors: Mantsyzov, A.B. / Birdsall, B. / Ivanova, E.V. / Alkalaeva, E.Z. / Krjuchkova, P.N. / Kelly, G. / Frolova, L.Yu. / I Polshakov, V.
#1: Journal: To be Published
Title: NMR assignments of the C-terminal domain of human polypeptide release factor eRF1.
Authors: Mantsyzov, A.B. / Ivanova, E.V. / Birdsall, B. / Kolosov, P.M. / Kisselev, L.L. / Polshakov, V.I.
History
DepositionFeb 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)19,8491
Polymers19,8491
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)24 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 19849.129 Da / Num. of mol.: 1 / Fragment: C-terminal Domain, residues 276-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Plasmid: pET23b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P62495

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: C-terminal domain of human translation termination factor eRF1, "closed" conformer
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-13C HSQC
1333D HNCA
1433D HN(CA)CB
1533D HN(CO)CA
1633D CBCA(CO)NH
1733D HBHA(CO)NH
1833D HNCO
1923D HNHA
11023D 1H-15N NOESY
11143D 1H-13C NOESY
11243D (H)CCH-TOCSY
11312D DQF-COSY
21452D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM C_ERF1_HUMAN-1, 50 mM potassium chloride-2, 10 mM potassium phosphate-3, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 15N] C_ERF1_HUMAN-4, 50 mM potassium chloride-5, 10 mM potassium phosphate-6, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-99% 13C; U-99% 15N] C_ERF1_HUMAN-7, 50 mM potassium chloride-8, 10 mM potassium phosphate-9, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-99% 13C; U-99% 15N] C_ERF1_HUMAN-10, 50 mM potassium chloride-11, 10 mM potassium phosphate-12, 100% D2O100% D2O
50.8 mM [U-99% 15N] C_ERF1_HUMAN-13, 50 mM potassium chloride-14, 10 mM potassium phosphate-15, 5 % C12E5/hexanol-16, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC_ERF1_HUMAN-11
50 mMpotassium chloride-21
10 mMpotassium phosphate-31
0.8 mMC_ERF1_HUMAN-4[U-99% 15N]2
50 mMpotassium chloride-52
10 mMpotassium phosphate-62
0.8 mMC_ERF1_HUMAN-7[U-99% 13C; U-99% 15N]3
50 mMpotassium chloride-83
10 mMpotassium phosphate-93
1 mMC_ERF1_HUMAN-10[U-99% 13C; U-99% 15N]4
50 mMpotassium chloride-114
10 mMpotassium phosphate-124
0.8 mMC_ERF1_HUMAN-13[U-99% 15N]5
50 mMpotassium chloride-145
10 mMpotassium phosphate-155
5 %C12E5/hexanol-165
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.087ambient 298 K
20.087ambient 311 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA7002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
Anglesearch2.1Polshakov VI & Feeney J.data analysis
CNS 2.1Linge, O'Donoghue and Nilgesstructure solution
ARIABRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 107 / Protein psi angle constraints total count: 107
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 24
NMR ensemble rmsDistance rms dev: 0.019 Å / Distance rms dev error: 0.001 Å

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