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- PDB-9q74: Crystal structure of T. brucei EIF4E5 in complex with EIF4G1 pept... -

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Basic information

Entry
Database: PDB / ID: 9q74
TitleCrystal structure of T. brucei EIF4E5 in complex with EIF4G1 peptide and cap-4.
Components
  • Eukaryotic translation initiation factor 4E type 5
  • MIF4G domain-containing protein
KeywordsTRANSLATION / TRANSLATION INITIATION FACTOR / EIF4E FAMILY / EIF4E5 / EIF4G1 / CAP-4
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
Chem-LRM / 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: 1.57 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)30,00513
Polymers27,5582
Non-polymers2,44711
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.380, 140.380, 41.350
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-404-

HOH

21A-472-

HOH

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Components

#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
#3: Chemical ChemComp-LRM / 2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-3H-purin-7-ium


Mass: 1826.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H79N20O38P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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, sitting drop
Details: Complex at 9.4 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization buffer containing 0.12 M monosaccharides (D-glucose, D-mannose, D- ...Details: Complex at 9.4 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization buffer containing 0.12 M monosaccharides (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (imidazole, MES), 30% precipitant Mix2 (ethylene glycol, PEG 8000) from Morpheus Screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.57→121.57 Å / Num. obs: 39727 / % possible obs: 94.4 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 1.57→1.8 Å / Num. unique obs: 1986 / CC1/2: 0.654

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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: 1.57→22.33 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.143 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18258 2027 5.1 %RANDOM
Rwork0.14239 ---
obs0.14444 37673 60.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.815 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.55 Å2-0 Å2
2---1.11 Å20 Å2
3---3.59 Å2
Refinement stepCycle: 1 / Resolution: 1.57→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 160 237 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122090
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161946
X-RAY DIFFRACTIONr_angle_refined_deg1.811.8292861
X-RAY DIFFRACTIONr_angle_other_deg0.591.7424495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.662512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86410333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02455
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_it10.7972.645950
X-RAY DIFFRACTIONr_mcbond_other10.7032.646950
X-RAY DIFFRACTIONr_mcangle_it16.3745.3071197
X-RAY DIFFRACTIONr_mcangle_other16.3845.3141198
X-RAY DIFFRACTIONr_scbond_it15.2583.7411140
X-RAY DIFFRACTIONr_scbond_other15.2533.7431141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other22.477.451661
X-RAY DIFFRACTIONr_long_range_B_refined30.46427.592467
X-RAY DIFFRACTIONr_long_range_B_other29.06326.122400
X-RAY DIFFRACTIONr_rigid_bond_restr7.87134036
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.609 Å
RfactorNum. reflection% reflection
Rfree0.099 2 -
Rwork0.316 21 -
obs--0.48 %
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)
10.86430.01680.10510.5140.00250.7550.04590.0473-0.0825-0.0293-0.00950.014-0.0115-0.0249-0.03640.01220.0139-0.00710.0174-0.00690.0144.701241.8308-6.1067
21.4832-0.811-0.1411.46040.01431.19870.07060.07110.0631-0.0457-0.0711-0.1003-0.14070.0380.00050.022-0.002-0.00030.00610.0060.010656.817850.07851.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 188
2X-RAY DIFFRACTION2B114 - 155

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