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- PDB-6g04: NMR Solution Structure of Yeast TSR2(1-152) in Complex with S26A(... -

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Basic information

Entry
Database: PDB / ID: 6g04
TitleNMR Solution Structure of Yeast TSR2(1-152) in Complex with S26A(100-119)
Components
  • 40S ribosomal protein S26-A
  • Pre-rRNA-processing protein TSR2
KeywordsTRANSPORT PROTEIN / ribosome maturation / transport of ribosomal protein S26 / nuclear unloading factor / escortin / nucleus / alpha-helical protein / eukaryotic specific segments
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome ...Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / ribosomal subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome binding / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-rRNA-processing protein TSR2 / Pre-rRNA-processing protein TSR2 / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e
Similarity search - Domain/homology
Small ribosomal subunit protein eS26A / Pre-rRNA-processing protein TSR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMichel, E. / Schuetz, S. / Damberger, F.F. / Allain, F.H.-T. / Panse, V.G.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilEURIBIO260676
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2.
Authors: Schutz, S. / Michel, E. / Damberger, F.F. / Oplova, M. / Pena, C. / Leitner, A. / Aebersold, R. / Allain, F.H. / Panse, V.G.
History
DepositionMar 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-rRNA-processing protein TSR2
B: 40S ribosomal protein S26-A


Theoretical massNumber of molelcules
Total (without water)20,8412
Polymers20,8412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2170 Å2
ΔGint-17 kcal/mol
Surface area11150 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pre-rRNA-processing protein TSR2 / 20S rRNA accumulation protein 2


Mass: 17938.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TSR2, YLR435W / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlusRIL / References: UniProt: Q06672
#2: Protein/peptide 40S ribosomal protein S26-A / Small ribosomal subunit protein eS26-A


Mass: 2903.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPS26A, RPS26, YGL189C, G1355 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlusRIL / References: UniProt: P39938

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D CBCA(CO)NH
131isotropic23D HBHA(CO)NH
141isotropic13D (H)CCH-TOCSY
151isotropic33D 1H-15N NOESY
161isotropic33D 1H-13C NOESY aliphatic
171isotropic33D 1H-13C NOESY aromatic
182isotropic43D HNCA
192isotropic43D CBCA(CO)NH
1102isotropic13D C(CO)NH
1112isotropic13D H(CCO)NH
1122isotropic33D 1H-15N NOESY
1132isotropic33D 1H-13C NOESY aliphatic
1142isotropic33D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] Tsr2(1-152), 0.5 mM S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2O13C,15N-Tsr2(1-152)_Unlabeled_S26A(100-119)95% H2O/5% D2O
solution20.5 mM Tsr2(1-152), 0.5 mM [U-13C; U-15N] S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2OUnlabeled-Tsr2(1-152)_13C,15N-S26A(100-119)95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTsr2(1-152)[U-13C; U-15N]1
0.5 mMS26A(100-119)natural abundance1
20 mMsodium phosphatenatural abundance1
1 mMDTT[U-2H]1
10 uMEDTAnatural abundance1
0.5 mMTsr2(1-152)natural abundance2
0.5 mMS26A(100-119)[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
1 mMDTT[U-2H]2
10 uMEDTAnatural abundance2
Sample conditionsIonic strength: 41 mM / Label: Default_Conditions / pH: 7 / Pressure: AMBIENT atm / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE9003
Bruker AVANCEBrukerAVANCE7004

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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