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- PDB-1rf8: Solution structure of the yeast translation initiation factor eIF... -

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Basic information

Entry
Database: PDB / ID: 1rf8
TitleSolution structure of the yeast translation initiation factor eIF4E in complex with m7GDP and eIF4GI residues 393 to 490
Components
  • Eukaryotic initiation factor 4F subunit p150
  • Eukaryotic translation initiation factor 4E
KeywordsBIOSYNTHETIC PROTEIN / TRANSLATION / Initiation factor / Protein biosynthesis / Translation regulation
Function / homology
Function and homology information


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 / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / positive regulation of endoplasmic reticulum unfolded protein response / mRNA cap binding / regulation of protein metabolic process / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / mTORC1-mediated signalling ...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 / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / positive regulation of endoplasmic reticulum unfolded protein response / mRNA cap binding / regulation of protein metabolic process / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / mTORC1-mediated signalling / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of translational initiation / 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 / cellular response to glucose starvation / translation initiation factor activity / stress granule assembly / ribosomal large subunit biogenesis / translational initiation / P-body / molecular condensate scaffold activity / cytoplasmic stress granule / regulation of cell cycle / ribosome / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm
Similarity search - Function
eIF4G, eIF4E-binding domain / Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e ...eIF4G, eIF4E-binding domain / Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Armadillo-type fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Chem-MTN / Eukaryotic translation initiation factor 4E / Eukaryotic initiation factor 4F subunit p150
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR
AuthorsGross, J.D. / Moerke, N.J. / von der Haar, T. / Lugovskoy, A.A. / Sachs, A.B. / McCarthy, J.E.G. / Wagner, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E.
Authors: Gross, J.D. / Moerke, N.J. / von der Haar, T. / Lugovskoy, A.A. / Sachs, A.B. / McCarthy, J.E. / Wagner, G.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Mar 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_spectrometer / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic initiation factor 4F subunit p150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8147
Polymers35,2992
Non-polymers1,5165
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 50structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein Eukaryotic translation initiation factor 4E / eIF4E / eIF-4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 24211.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIF45, CDC33, YOL139C / Plasmid: PET30a / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P07260
#2: Protein Eukaryotic initiation factor 4F subunit p150 / eIF4F p150 / eIF-4F p150 / mRNA cap-binding protein complex subunit p150


Mass: 11087.355 Da / Num. of mol.: 1 / Fragment: residues 391-488 (SWS:P39935)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIF4631, YGR162W / Plasmid: pGEX-2T / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P39935
#3: Chemical
ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18NO3S2
#4: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.6 mM 1:1:1 m7GDP/eIF4E/eIF4G(393-490) complex
Solvent system: 50 mM Sodium Phosphate 50 mM KCl 12 mM CHAPS
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Bruker AVANCEBrukerAVANCE5002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 11

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