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- PDB-6z29: Structure of eIF4G1 (37-49) - PUB1 RRM3 chimera in solution -

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Basic information

Entry
Database: PDB / ID: 6z29
TitleStructure of eIF4G1 (37-49) - PUB1 RRM3 chimera in solution
ComponentsEukaryotic initiation factor 4F subunit p150,Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
KeywordsTRANSLATION / Stress Granules / Translation Regulation
Function / homology
Function and homology information


Deadenylation of mRNA / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / regulation of protein metabolic process / positive regulation of endoplasmic reticulum unfolded protein response / mTORC1-mediated signalling / poly(U) RNA binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...Deadenylation of mRNA / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / regulation of protein metabolic process / positive regulation of endoplasmic reticulum unfolded protein response / mTORC1-mediated signalling / poly(U) RNA binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ATPase activator activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / stress granule assembly / translational initiation / regulation of mRNA stability / translation initiation factor activity / ribosomal large subunit biogenesis / molecular condensate scaffold activity / P-body / cytoplasmic stress granule / : / ribosome / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / Initiation factor 4G / MIF4G domain / RNA recognition motif domain, eukaryote / RNA recognition motif / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA recognition motif ...Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / Initiation factor 4G / MIF4G domain / RNA recognition motif domain, eukaryote / RNA recognition motif / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 / Eukaryotic initiation factor 4F subunit p150
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChaves-Arquero, B. / Martinez-Lumbreras, S. / Perez-Canadillas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)CTQ2018 84371 Spain
CitationJournal: Front Mol Biosci / Year: 2022
Title: eIF4G1 N-terminal intrinsically disordered domain is a multi-docking station for RNA, Pab1, Pub1, and self-assembly.
Authors: Chaves-Arquero, B. / Martinez-Lumbreras, S. / Sibille, N. / Camero, S. / Bernado, P. / Jimenez, M.A. / Zorrilla, S. / Perez-Canadillas, J.M.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic initiation factor 4F subunit p150,Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1


Theoretical massNumber of molelcules
Total (without water)13,0321
Polymers13,0321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8280 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic initiation factor 4F subunit p150,Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 / / eIF4F p150 / eIF4G1 / mRNA cap-binding protein complex subunit p150 / ARS consensus-binding protein ...eIF4F p150 / eIF4G1 / mRNA cap-binding protein complex subunit p150 / ARS consensus-binding protein ACBP-60 / Poly uridylate-binding protein / Poly(U)-binding protein


Mass: 13031.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TIF4631, YGR162W, PUB1, RNP1, YNL016W, N2842 / Production host: Escherichia coli (E. coli) / References: UniProt: P39935, UniProt: P32588

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
313isotropic12D 1H-15N HSQC
323isotropic12D 1H-13C HSQC aliphatic
333isotropic13D HNCO
343isotropic13D HNCA
363isotropic13D CBCA(CO)NH
191isotropic12D 1H-1H NOESY
2102isotropic12D 1H-1H NOESY
1111isotropic12D 1H-1H TOCSY
2122isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1250 uM eIF4G1(37-49)/PUB1(RRM3) Chimera, 25 mM potassium phosphate, 25 mM sodium chloride, 0.1 mM DTT, 90% H2O/10% D2OH2O90% H2O/10% D2O
solution2250 uM eIF4G1(37-49)/PUB1(RRM3) Chimera, 25 mM potassium phosphate, 25 mM sodium chloride, 0.1 mM DTT, 100% D2OD2O100% D2O
solution3148 uM [U-13C; U-15N] eIF4G1(37-49)/PUB1(RRM3) Chimera, 25 mM potassium phosphate, 25 mM sodium chloride, 0.1 mM DTT, 90% H2O/10% D2O15N13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMeIF4G1(37-49)/PUB1(RRM3) Chimeranatural abundance1
25 mMpotassium phosphatenatural abundance1
25 mMsodium chloridenatural abundance1
0.1 mMDTTnatural abundance1
250 uMeIF4G1(37-49)/PUB1(RRM3) Chimeranatural abundance2
25 mMpotassium phosphatenatural abundance2
25 mMsodium chloridenatural abundance2
0.1 mMDTTnatural abundance2
148 uMeIF4G1(37-49)/PUB1(RRM3) Chimera[U-13C; U-15N]3
25 mMpotassium phosphatenatural abundance3
25 mMsodium chloridenatural abundance3
0.1 mMDTTnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.050 Mconditions15.0 1 atm301.2 K
20.050 Mconditions25.0 1 atm301.2 K
30.050 Mcondicions35.0 1 atm301.2 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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