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- PDB-2llx: Solution structure of the N-terminal domain of human polypeptide ... -

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Basic information

Entry
Database: PDB / ID: 2llx
TitleSolution structure of the N-terminal domain of human polypeptide chain release factor eRF1
ComponentsEukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION / protein synthesis termination / stop codon recognition
Function / homology
Function and homology information


translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / peptidyl-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 detailsclosest to the average, model 1
AuthorsPolshakov, V.I. / Eliseev, B.D. / Birdsall, B. / Frolova, L.Y.
CitationJournal: Protein Sci. / Year: 2012
Title: Structure and dynamics in solution of the stop codon decoding N-terminal domain of the human polypeptide chain release factor eRF1.
Authors: Polshakov, V.I. / Eliseev, B.D. / Birdsall, B. / Frolova, L.Y.
History
DepositionNov 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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

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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)16,7691
Polymers16,7691
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 / 50structures 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 / Protein Cl1 / TB3-1


Mass: 16769.348 Da / Num. of mol.: 1 / Fragment: UNP residues 1-142
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) / Strain (production host): BL21(DE3) / Variant (production host): pUBS / References: UniProt: P62495

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1212D 1H-13C HSQC
1332D DQF-COSY
1432D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CB
1813D HBHA(CO)NH
1943D HNHA
11043D HNHB
11113D H(CCO)NH
11223D (H)CCH-TOCSY
11343D 1H-15N NOESY
11423D 1H-13C NOESY
11552D IPAP
11642D J-MODULATED 1H-15N HSQC
117415N{1H} NOE
118415N T1
119415N T2

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] NeRF1, 25 mM sodium chloride, 10 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] NeRF1, 25 mM sodium chloride, 10 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.01 % sodium azide, 100% D2O100% D2O
31 mM NeRF1, 25 mM sodium chloride, 10 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.01 % sodium azide, 100% D2O100% D2O
41 mM [U-99% 15N] NeRF1, 25 mM sodium chloride, 10 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
51 mM [U-99% 15N] NeRF1, 25 mM sodium chloride, 10 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.01 % sodium azide, 5.00 % C12E5, 1.068 % hexanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNeRF1-1[U-99% 13C; U-99% 15N]1
25 mMsodium chloride-21
10 mMsodium phosphate-31
2 mMbeta-mercaptoethanol-41
0.01 %sodium azide-51
1 mMNeRF1-6[U-99% 13C; U-99% 15N]2
25 mMsodium chloride-72
10 mMsodium phosphate-82
2 mMbeta-mercaptoethanol-92
0.01 %sodium azide-102
1 mMNeRF1-113
25 mMsodium chloride-123
10 mMsodium phosphate-133
2 mMbeta-mercaptoethanol-143
0.01 %sodium azide-153
1 mMNeRF1-16[U-99% 15N]4
25 mMsodium chloride-174
10 mMsodium phosphate-184
2 mMbeta-mercaptoethanol-194
0.01 %sodium azide-204
1 mMNeRF1-21[U-99% 15N]5
25 mMsodium chloride-225
10 mMsodium phosphate-235
2 mMbeta-mercaptoethanol-245
0.01 %sodium azide-255
5.00 %C12E5-265
1.068 %hexanol-275
Sample conditionsIonic strength: 0.035 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
VNMRVariancollection
NMRPipe5.99Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.114Goddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
Anglesearch2.1Polshakov, Feeneydata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRest0.99Polshakovdata analysis
RelaxFit0.99Polshakovdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
Insight II2000Accelrys Software Inc.data analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2669 / NOE intraresidue total count: 975 / NOE long range total count: 524 / NOE medium range total count: 494 / NOE sequential total count: 638 / Protein chi angle constraints total count: 64 / Protein phi angle constraints total count: 126 / Protein psi angle constraints total count: 126
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 2 ° / Maximum upper distance constraint violation: 0.1 Å
NMR ensemble rmsDistance rms dev: 0.0059 Å / Distance rms dev error: 0.0005 Å

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