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- PDB-9q73: Crystal structure of T. brucei EIF4E5 in complex with EIF4G1 peptide -

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Basic information

Entry
Database: PDB / ID: 9q73
TitleCrystal structure of T. brucei EIF4E5 in complex with EIF4G1 peptide
Components
  • Eukaryotic translation initiation factor 4E type 5
  • MIF4G domain-containing protein
KeywordsTRANSLATION / TRANSLATION INITIATION FACTOR / EIF4E FAMILY / EIF4E5 / EIF4G1
Function / homology
Function and homology information


RNA cap 4 binding / eukaryotic translation initiation factor 4F complex / nuclear lumen / RNA 7-methylguanosine cap binding / ciliary plasm / post-transcriptional regulation of gene expression / translation initiation factor activity / cell motility / translational initiation / cytoplasmic stress granule ...RNA cap 4 binding / eukaryotic translation initiation factor 4F complex / nuclear lumen / RNA 7-methylguanosine cap binding / ciliary plasm / post-transcriptional regulation of gene expression / translation initiation factor activity / cell motility / translational initiation / cytoplasmic stress granule / translation / mRNA binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
1-BUTANOL / 1,3-PROPANDIOL / Eukaryotic translation initiation factor 4E type 5 / MIF4G domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsPenteado, R.F. / Guimaraes, B.G.
Funding support France, Brazil, 2items
OrganizationGrant numberCountry
Pasteur Institute France
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Selective eIF4E-eIF4G Pairing and Cap-4 Recognition Mechanisms in Trypanosomatids: Insights From EIF4E5-EIF4G1 and EIF4E6-EIF4G5 Complexes.
Authors: Penteado, R.F. / Vichier-Guerre, S. / da Silva Pereira, B.M. / Dugue, L. / Guerra Slompo, E.P. / Assuncao de Matos, T.R. / Pochet, S. / Zanchin, N.I.T. / Guimaraes, B.G.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 5
B: MIF4G domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7325
Polymers27,5582
Non-polymers1733
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-13 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.410, 140.410, 41.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-203-

NA

21A-330-

HOH

31A-469-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Eukaryotic translation initiation factor 4E type 5


Mass: 22007.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb10.70.2180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38B99
#2: Protein/peptide MIF4G domain-containing protein


Mass: 5551.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb05.30H13.650, Tb927.5.1490 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57VB4

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Non-polymers , 4 types, 235 molecules

#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Complex at 9.1 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 with crystallization solution containing 0.3 M Carboxylic Acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M ...Details: Complex at 9.1 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 with crystallization solution containing 0.3 M Carboxylic Acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.12 M Alcohols (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), 0.1 M Buffer System 1 (pH 6.5; 0.4 M imidazole, 0.6 M MES monohydrate), and 35% Precipitant Mix 4 (25% v/v MPD, 25% v/v PEG 1000, 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.66→121.6 Å / Num. obs: 39342 / % possible obs: 95.3 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 1.66→1.83 Å / Num. unique obs: 1967 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→18.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 4.163 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15688 2014 5.1 %RANDOM
Rwork0.13718 ---
obs0.1382 37279 71.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0.64 Å2-0 Å2
2---1.28 Å20 Å2
3---4.16 Å2
Refinement stepCycle: 1 / Resolution: 1.66→18.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 11 232 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121973
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161888
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.8232701
X-RAY DIFFRACTIONr_angle_other_deg0.3861.7524365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.083513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91510342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022364
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it27.982.776964
X-RAY DIFFRACTIONr_mcbond_other27.8642.775964
X-RAY DIFFRACTIONr_mcangle_it36.4585.5971220
X-RAY DIFFRACTIONr_mcangle_other36.4755.6111221
X-RAY DIFFRACTIONr_scbond_it12.4083.2221009
X-RAY DIFFRACTIONr_scbond_other12.4073.2291010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.3016.4561473
X-RAY DIFFRACTIONr_long_range_B_refined43.34624.722313
X-RAY DIFFRACTIONr_long_range_B_other42.96923.482266
X-RAY DIFFRACTIONr_rigid_bond_restr9.5433861
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.702 Å
RfactorNum. reflection% reflection
Rfree0.183 9 -
Rwork0.256 188 -
obs--4.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9019-0.4852-0.00871.2528-0.0930.7916-0.0037-0.0386-0.09270.02930.030.05840.0123-0.01-0.02630.0275-0.0011-0.00130.05690.00790.010814.297960.0346.4759
22.6342-0.7287-0.84790.99590.1590.9625-0.0279-0.05910.2042-0.01420.0555-0.0509-0.07820.0514-0.02760.053-0.009-0.00730.04630.00030.018215.005674.3721-1.6063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 187
2X-RAY DIFFRACTION2B114 - 154

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