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- PDB-2w97: Crystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide -

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Basic information

Entry
Database: PDB / ID: 2w97
TitleCrystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide
Components(EUKARYOTIC TRANSLATION INITIATION FACTOR ...) x 3
KeywordsTRANSLATION / PROTEIN BIOSYNTHESIS / INITIATION FACTOR / TRANSLATION REGULATION
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / : / positive regulation of translation in response to endoplasmic reticulum stress / macromolecule biosynthetic process / cap-dependent translational initiation / eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / regulation of translation at postsynapse, modulating synaptic transmission ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / : / positive regulation of translation in response to endoplasmic reticulum stress / macromolecule biosynthetic process / cap-dependent translational initiation / eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / mRNA cap binding / Deadenylation of mRNA / negative regulation of peptidyl-threonine phosphorylation / miRNA-mediated gene silencing by inhibition of translation / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / regulation of translational initiation / positive regulation of protein localization to cell periphery / stem cell population maintenance / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mTORC1-mediated signalling / positive regulation of protein metabolic process / regulation of presynapse assembly / negative regulation of neuron differentiation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / L13a-mediated translational silencing of Ceruloplasmin expression / cellular response to nutrient levels / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / positive regulation of peptidyl-serine phosphorylation / translation initiation factor binding / translation initiation factor activity / positive regulation of neuron differentiation / positive regulation of mitotic cell cycle / negative regulation of autophagy / cellular response to dexamethasone stimulus / AUF1 (hnRNP D0) binds and destabilizes mRNA / translational initiation / lung development / P-body / ISG15 antiviral mechanism / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / positive regulation of cell growth / DNA-binding transcription factor binding / molecular adaptor activity / response to ethanol / postsynapse / negative regulation of translation / nuclear speck / ribosome / translation / mRNA binding / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / Translation Initiation factor eIF- 4e-like / W2 domain ...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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / Translation Initiation factor eIF- 4e-like / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MGO / TRIETHYLENE GLYCOL / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBrown, C.J. / Verma, C.S. / Walkinshaw, M.D. / Lane, D.P.
CitationJournal: Cell Cycle / Year: 2009
Title: Crystallization of eIF4E complexed with eIF4GI peptide and glycerol reveals distinct structural differences around the cap-binding site.
Authors: Brown, C.J. / Verma, C.S. / Walkinshaw, M.D. / Lane, D.P.
History
DepositionJan 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 TRANSLATION INITIATION FACTOR 4E
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,23412
Polymers53,9784
Non-polymers1,2568
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-19.7 kcal/mol
Surface area23980 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.106, 38.201, 93.687
Angle α, β, γ (deg.)90.00, 101.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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EUKARYOTIC TRANSLATION INITIATION FACTOR ... , 3 types, 4 molecules ABEF

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / MRNA CAP-BINDING PROTEIN / EIF-4F 25 KDA SUBUNIT / EIF-4E / EIF4E


Mass: 25130.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P06730
#2: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / MRNA CAP-BINDING PROTEIN / EIF-4F 25 KDA SUBUNIT / EIF-4E / EIF4E


Mass: 25145.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P06730
#3: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1 / P220 / EIF-4-GAMMA 1 / EIF-4G 1 / EIF-4G1 / EIF4GI


Mass: 1851.155 Da / Num. of mol.: 2 / Fragment: EIF4GI BINDING MOTIF, RESIDUES 413-426 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q04637

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Non-polymers , 5 types, 173 molecules

#4: Chemical ChemComp-MGO / [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE


Mass: 537.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O14P3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 % / Description: NONE
Crystal growpH: 8
Details: 60% AMMONIUM SULPHATE, 100MM TRIS-HCL PH 8.0, 1% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26638 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8W

2v8w


Resolution: 2.29→28.02 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.455 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1341 5 %RANDOM
Rwork0.197 ---
obs0.199 25283 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.29→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 75 165 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9594581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18223.353173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70615594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1551528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022543
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22266
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8691.51979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53123110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93231650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2354.51471
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 103 -
Rwork0.222 1602 -
obs--87.39 %

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