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- PDB-9q79: Crystal structure of T. cruzi EIF4E6 in complex with EIF4G5 pepti... -

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Basic information

Entry
Database: PDB / ID: 9q79
TitleCrystal structure of T. cruzi EIF4E6 in complex with EIF4G5 peptide and cap-4
Components
  • Eukaryotic translation initiation factor 4 gamma 5
  • Putative Eukaryotic translation initiation factor 4E type 6
KeywordsTRANSLATION / TRANSLATION INITIATION FACTOR / EIF4E FAMILY / EIF4E6 / EIF4G5 / CAP-4
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / translation initiation factor activity / mRNA binding
Similarity search - Function
Translation Initiation factor eIF- 4e-like / MIF4G domain / MIF4G-like, type 3 / Armadillo-type fold
Similarity search - Domain/homology
CITRATE ANION / Chem-LRM / Eukaryotic translation initiation factor 4 gamma 5 / Putative Eukaryotic translation initiation factor 4E type 6
Similarity search - Component
Biological speciesTrypanosoma cruzi Dm28c (eukaryote)
Trypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: Putative Eukaryotic translation initiation factor 4E type 6
C: Putative Eukaryotic translation initiation factor 4E type 6
G: Putative Eukaryotic translation initiation factor 4E type 6
B: Eukaryotic translation initiation factor 4 gamma 5
D: Eukaryotic translation initiation factor 4 gamma 5
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,27311
Polymers108,4318
Non-polymers3,8413
Water2,666148
1
A: Putative Eukaryotic translation initiation factor 4E type 6
B: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers27,1082
Non-polymers1,8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-25 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: Putative Eukaryotic translation initiation factor 4E type 6
D: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers27,1082
Non-polymers1,8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-26 kcal/mol
Surface area10840 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 area2660 Å2
ΔGint-27 kcal/mol
Surface area10190 Å2
MethodPISA
4
E: Putative Eukaryotic translation initiation factor 4E type 6
F: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2973
Polymers27,1082
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-23 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.211, 93.236, 119.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 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.: 2 / Source method: obtained synthetically / Formula: C56H79N20O38P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.11 %
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 (pre-incubated with cap-4) with crystallization buffer containing 100 mM tri-sodium citrate (pH 3.5) and 20.6% 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: 2.3→119.65 Å / Num. obs: 30384 / % possible obs: 96.1 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.39 Å / Num. unique obs: 1520 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.62 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 1558 5.14 %
Rwork0.234 --
obs0.2376 30338 73.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 253 148 7049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097211
X-RAY DIFFRACTIONf_angle_d1.249872
X-RAY DIFFRACTIONf_dihedral_angle_d19.1892769
X-RAY DIFFRACTIONf_chiral_restr0.0511087
X-RAY DIFFRACTIONf_plane_restr0.0071232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.3785750.2631220X-RAY DIFFRACTION35
2.37-2.460.3184700.26191537X-RAY DIFFRACTION44
2.46-2.560.3784900.28341726X-RAY DIFFRACTION50
2.56-2.670.31541030.29011937X-RAY DIFFRACTION55
2.67-2.810.361160.30562213X-RAY DIFFRACTION63
2.82-2.990.40141310.27652633X-RAY DIFFRACTION75
2.99-3.220.30421730.25783146X-RAY DIFFRACTION90
3.22-3.550.32622050.23433505X-RAY DIFFRACTION100
3.55-4.060.28262050.19533548X-RAY DIFFRACTION100
4.06-5.110.2381990.18583584X-RAY DIFFRACTION100
5.11-46.620.31511910.24713731X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.0831 Å / Origin y: 13.1792 Å / Origin z: -16.8649 Å
111213212223313233
T0.0817 Å20.094 Å2-0.1041 Å2-0.108 Å2-0.0313 Å2--0.2843 Å2
L0.0965 °2-0.1432 °20.0381 °2-0.4443 °2-0.073 °2---0.0372 °2
S0.0045 Å °0.0595 Å °0.0402 Å °0.1355 Å °-0.03 Å °0.3402 Å °-0.0428 Å °-0.0636 Å °-0.3034 Å °
Refinement TLS groupSelection details: all

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