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- PDB-9q78: Crystal structure of T. cruzi EIF4E6 in complex with EIF4G5 peptide -

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Basic information

Entry
Database: PDB / ID: 9q78
TitleCrystal structure of T. cruzi EIF4E6 in complex with EIF4G5 peptide
Components
  • Eukaryotic translation initiation factor 4 gamma 5
  • Putative Eukaryotic translation initiation factor 4E type 6
KeywordsTRANSLATION / TRANSLATION INITIATION FACTOR / EIF4E FAMILY / EIF4E6 / EIF4G5
Function / homologyTranslation Initiation factor eIF- 4e-like / MIF4G domain / eukaryotic translation initiation factor 4F complex / MIF4G-like, type 3 / translation initiation factor activity / Armadillo-type fold / mRNA binding / Eukaryotic translation initiation factor 4 gamma 5 / Putative Eukaryotic translation initiation factor 4E type 6
Function and homology information
Biological speciesTrypanosoma cruzi Dm28c (eukaryote)
Trypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
C: Putative Eukaryotic translation initiation factor 4E type 6
D: Eukaryotic translation initiation factor 4 gamma 5
A: Putative Eukaryotic translation initiation factor 4E type 6
B: Eukaryotic translation initiation factor 4 gamma 5
G: Putative Eukaryotic translation initiation factor 4E type 6
H: Eukaryotic translation initiation factor 4 gamma 5
E: Putative Eukaryotic translation initiation factor 4E type 6
F: Eukaryotic translation initiation factor 4 gamma 5


Theoretical massNumber of molelcules
Total (without water)108,4318
Polymers108,4318
Non-polymers00
Water4,216234
1
C: Putative Eukaryotic translation initiation factor 4E type 6
D: Eukaryotic translation initiation factor 4 gamma 5


Theoretical massNumber of molelcules
Total (without water)27,1082
Polymers27,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-28 kcal/mol
Surface area9870 Å2
MethodPISA
2
A: Putative Eukaryotic translation initiation factor 4E type 6
B: Eukaryotic translation initiation factor 4 gamma 5


Theoretical massNumber of molelcules
Total (without water)27,1082
Polymers27,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-26 kcal/mol
Surface area9770 Å2
MethodPISA
3
G: Putative Eukaryotic translation initiation factor 4E type 6
H: Eukaryotic translation initiation factor 4 gamma 5


Theoretical massNumber of molelcules
Total (without water)27,1082
Polymers27,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-27 kcal/mol
Surface area9720 Å2
MethodPISA
4
E: Putative Eukaryotic translation initiation factor 4E type 6
F: Eukaryotic translation initiation factor 4 gamma 5


Theoretical massNumber of molelcules
Total (without water)27,1082
Polymers27,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-29 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.893, 112.694, 100.024
Angle α, β, γ (deg.)90.00, 97.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative Eukaryotic translation initiation factor 4E type 6


Mass: 21401.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi Dm28c (eukaryote) / Gene: C4B63_8g546 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2VTW2
#2: Protein/peptide
Eukaryotic translation initiation factor 4 gamma 5


Mass: 5706.448 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_21g47 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2VHI6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Complex at 7.3 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 with crystallization buffer containing 80 mM Monosaccharides (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M ...Details: Complex at 7.3 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 with crystallization buffer containing 80 mM Monosaccharides (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 100 mM Buffer System 1 (pH 6.5; 0.4 M imidazole, 0.6 M MES monohydrate), and 37.5% (w/v) 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: Jul 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→112.69 Å / Num. obs: 37674 / % possible obs: 94.4 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.19 Å / Num. unique obs: 1884 / CC1/2: 0.767

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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: 2.1→49.58 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.892 / SU B: 18.676 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26977 1932 5.1 %RANDOM
Rwork0.20108 ---
obs0.20454 35742 73.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-1.28 Å2
2--4.23 Å20 Å2
3----3.58 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 0 234 6746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126662
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166191
X-RAY DIFFRACTIONr_angle_refined_deg0.841.8279121
X-RAY DIFFRACTIONr_angle_other_deg0.31.74714232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4835813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.189539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.155101004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027808
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021560
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_it4.7172.0543222
X-RAY DIFFRACTIONr_mcbond_other4.7132.0543222
X-RAY DIFFRACTIONr_mcangle_it7.4024.1284018
X-RAY DIFFRACTIONr_mcangle_other7.4024.1294019
X-RAY DIFFRACTIONr_scbond_it4.6952.1613440
X-RAY DIFFRACTIONr_scbond_other4.6942.1623441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1164.3915095
X-RAY DIFFRACTIONr_long_range_B_refined39.85817.147547
X-RAY DIFFRACTIONr_long_range_B_other39.08617.127535
X-RAY DIFFRACTIONr_rigid_bond_restr5.443312853
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 72 -
Rwork0.261 933 -
obs--27.18 %
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)
11.40220.1242-0.13361.10170.10930.72050.00960.04940.1886-0.13630.0301-0.0417-0.0506-0.0356-0.03970.0613-0.01340.00990.01220.02750.12795.225636.549240.0541
21.5298-0.39870.54762.6414-0.03610.9316-0.0083-0.05280.0253-0.3237-0.0486-0.26310.1176-0.11490.05690.0792-0.01650.05660.02810.00850.085213.240225.034837.6557
32.08520.3305-0.04141.3507-0.44020.7317-0.06160.0189-0.2135-0.17240.04240.00610.1829-0.01720.01910.0571-0.00720.00390.0052-0.01830.11290.47171.848643.6679
42.80430.0336-0.98290.8985-1.44982.7701-0.073-0.01840.1029-0.05230.0770.04170.0539-0.0335-0.0040.1085-0.0491-0.03140.06730.03040.1269-7.19313.145140.3333
51.70590.1052-0.00891.12210.01270.92420.01040.03470.1884-0.1019-0.0086-0.0235-0.074-0.0055-0.00190.073-0.00850.01060.00460.01540.0992-7.454340.2884-8.6283
61.72070.2919-0.47222.37920.63441.18050.0108-0.0775-0.0118-0.2102-0.0318-0.17440.01260.00190.0210.0742-0.0080.04060.00570.00120.05120.259128.5087-9.9214
71.48530.2253-0.00061.7181-0.11440.9137-0.013-0.0734-0.1242-0.189-0.03770.04460.1558-0.00020.05070.0582-0.00090.01340.0057-0.00340.0834-12.715.7172-6.6328
81.96070.0432-0.52831.5141-1.17671.81020.0228-0.07760.1738-0.16520.0640.1504-0.0604-0.0735-0.08680.1141-0.019-0.04740.0185-0.00730.0933-20.30416.9982-9.7443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 180
2X-RAY DIFFRACTION2B75 - 112
3X-RAY DIFFRACTION3C8 - 179
4X-RAY DIFFRACTION4D75 - 114
5X-RAY DIFFRACTION5E8 - 180
6X-RAY DIFFRACTION6F75 - 114
7X-RAY DIFFRACTION7G8 - 179
8X-RAY DIFFRACTION8H76 - 113

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