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- PDB-2ktv: Human eRF1 C-domain, "open" conformer -

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Basic information

Entry
Database: PDB / ID: 2ktv
TitleHuman eRF1 C-domain, "open" conformer
ComponentsEukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION / eRF1 / C domain / termination / Eukaryotes / 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 / translation release factor activity, codon specific / protein methylation / 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 / translation release factor activity, codon specific / protein methylation / 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
AuthorsMantsyzov, A.B. / Polshakov, V.I. / Birdsall, B.
Citation
Journal: Febs J. / Year: 2010
Title: NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor.
Authors: Mantsyzov, A.B. / Ivanova, E.V. / Birdsall, B. / Alkalaeva, E.Z. / Kryuchkova, P.N. / Kelly, G. / Frolova, L.Y. / Polshakov, V.I.
#1: Journal: Biomol.Nmr Assign. / Year: 2007
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 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct / 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_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _struct.pdbx_model_details / _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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1222D 1H-15N HSQC
1333D HNCA
1433D HN(CA)CB
1533D HN(CO)CA
1633D CBCA(CO)NH
1733D HBHA(CO)NH
1833D HNCO
1933D HNHA
11033D 1H-15N NOESY
11133D 1H-13C NOESY
11233D (H)CCH-TOCSY
11343D HNCA
11443D HN(CA)CB
11543D HN(CO)CA
11643D CBCA(CO)NH
11743D HBHA(CO)NH
11843D HNCO
11943D HNHA
12043D 1H-15N NOESY
12143D 1H-13C NOESY
12243D (H)CCH-TOCSY
12352D 1H-13C HSQC
22433D 1H-15N NOESY
22533D 1H-13C NOESY
22643D 1H-15N NOESY
22743D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 MM C_ERF1_HUMAN, 50 MM POTASSIUM CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.8 MM [U-99% 15N] C_ERF1_HUMAN, 50 MM POTASSIUM CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.8 MM [U-99% 13C U-99% 15N] C_ERF1_HUMAN, 50 MM POTASSIUM CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution40.8 MM [U-99% 13C U-99% 15N] C_ERF1_HUMAN, 50 MM POTASSIUM CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 100% D2Osample_490% H2O/10% D2O
bicelle51 MM C_ERF1_ HUMAN, 50 MM POTASSIUM CHLORIDE, 10 MM POTASSIUM PHOSPHATE, 5 % DMPC/DHPC/ SDS, 90% H2O/10% D2Osample_590% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC_ERF1_HUMANnatural abundance1
50 mMpotassium chloridenatural abundance1
10 mMpotassium phosphatenatural abundance1
0.8 mMC_ERF1_HUMAN[U-99% 15N]2
50 mMpotassium chloridenatural abundance2
10 mMpotassium phosphatenatural abundance2
0.8 mMC_ERF1_HUMAN[U-99% 13C; U-99% 15N]3
50 mMpotassium chloridenatural abundance3
10 mMpotassium phosphatenatural abundance3
0.8 mMC_ERF1_HUMAN[U-99% 13C; U-99% 15N]4
50 mMpotassium chloridenatural abundance4
10 mMpotassium phosphatenatural abundance4
1 mMC_ERF1_HUMANnatural abundance5
50 mMpotassium chloridenatural abundance5
10 mMpotassium phosphatenatural abundance5
5 %DMPC/DHPC/SDSnatural abundance5
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
Bruker AVANCEBrukerAVANCE7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE- KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
VNMRVariancollection
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
Anglesearch2.1Polshakov VI & Feeney J.data analysis
CNS2.1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE- KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENstructure solution
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 108 / Protein psi angle constraints total count: 108
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: 0.017 Å / Distance rms dev error: 0.001 Å

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