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- PDB-9q75: Crystal structure of T. cruzi EIF4E5 in complex with EIF4G1 pepti... -

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Basic information

Entry
Database: PDB / ID: 9q75
TitleCrystal structure of T. cruzi EIF4E5 in complex with EIF4G1 peptide and cap-4.
Components
  • Eukaryotic translation initiation factor 4 gamma 1
  • Putative Eukaryotic translation initiation factor 4E type 5
KeywordsTRANSLATION / TRANSLATION INITIATION FACTOR / EIF4E FAMILY / EIF4E5 / EIF4G1 / CAP-4
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / mRNA binding
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 4 gamma 1 / Putative Eukaryotic translation initiation factor 4E type 5
Similarity search - Component
Biological speciesTrypanosoma cruzi Dm28c (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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: Putative Eukaryotic translation initiation factor 4E type 5
C: Putative Eukaryotic translation initiation factor 4E type 5
E: Putative Eukaryotic translation initiation factor 4E type 5
B: Eukaryotic translation initiation factor 4 gamma 1
D: Eukaryotic translation initiation factor 4 gamma 1
F: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,36313
Polymers85,2316
Non-polymers4,1337
Water10,305572
1
A: Putative Eukaryotic translation initiation factor 4E type 5
B: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6985
Polymers28,4102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-55 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: Putative Eukaryotic translation initiation factor 4E type 5
D: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3324
Polymers28,4102
Non-polymers1,9222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-25 kcal/mol
Surface area11970 Å2
MethodPISA
3
E: Putative Eukaryotic translation initiation factor 4E type 5
F: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3324
Polymers28,4102
Non-polymers1,9222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-26 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.380, 88.889, 110.165
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 5


Mass: 22611.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi Dm28c (eukaryote) / Gene: C3747_7g399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2XI07
#2: Protein/peptide Eukaryotic translation initiation factor 4 gamma 1


Mass: 5798.608 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi Dm28c (eukaryote) / Gene: C4B63_83g34 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2UXK5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Complex at 16 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 0.29 M (NH4)2SO4; 0.1 M Tris-HCl pH 8.5; 26% (m/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: 1.77→69.18 Å / Num. obs: 67238 / % possible obs: 95.8 % / Redundancy: 13.9 % / CC1/2: 0.999 / Net I/σ(I): 16.7
Reflection shellResolution: 1.77→1.9 Å / Num. unique obs: 3362 / CC1/2: 0.773

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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: 1.77→25.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.333 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21501 3398 5.1 %RANDOM
Rwork0.15763 ---
obs0.16052 63798 78.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0 Å2
2---5.25 Å20 Å2
3---5.71 Å2
Refinement stepCycle: 1 / Resolution: 1.77→25.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 265 572 6330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165626
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.8298703
X-RAY DIFFRACTIONr_angle_other_deg0.5421.74412925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.414547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03910906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021488
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_it9.0773.5282799
X-RAY DIFFRACTIONr_mcbond_other9.0493.5282799
X-RAY DIFFRACTIONr_mcangle_it13.4327.1273508
X-RAY DIFFRACTIONr_mcangle_other13.4367.1293509
X-RAY DIFFRACTIONr_scbond_it19.5134.1013497
X-RAY DIFFRACTIONr_scbond_other19.4474.0913494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other25.0038.3215177
X-RAY DIFFRACTIONr_long_range_B_refined28.97432.427534
X-RAY DIFFRACTIONr_long_range_B_other28.31731.747410
X-RAY DIFFRACTIONr_rigid_bond_restr7.659311922
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 20 -
Rwork0.266 391 -
obs--6.63 %
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)
11.4829-0.14620.66461.42-0.00211.5535-0.0274-0.0406-0.0867-0.0229-0.01670.17070.0738-0.06420.0440.0325-0.01330.01370.0829-0.04460.0509-4.4327-2.8773-22.8005
23.7216-0.95770.70790.9221-0.19441.0499-0.2024-0.2710.1860.12560.07050.0219-0.211-0.05030.13190.08240.0064-0.03620.0621-0.04510.0664-4.944412.0771-19.4256
30.95840.45530.27831.29260.24151.5029-0.02350.1052-0.042-0.126-0.0057-0.0485-0.09760.14020.02920.0236-0.00690.0050.1084-0.0110.006923.620410.2723.3643
41.27750.71330.26492.96411.6041.03830.0669-0.09930.04510.0086-0.13530.1423-0.03970.01230.06840.0468-0.04430.00450.1248-0.01530.007620.161711.023618.3755
51.15250.2799-0.14071.2033-0.51581.45160.0074-0.0225-0.0449-0.03720.0456-0.04860.06280.0777-0.0530.03650.00450.02180.0562-0.00910.0247-3.5327-17.056216.2866
60.9543-0.0826-0.9342.0238-0.0483.20630.02930.09620.125-0.06680.07010.1875-0.2655-0.0353-0.09940.02930.001-0.00520.10470.06280.0727-18.4084-13.473116.9466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 186
2X-RAY DIFFRACTION2B106 - 147
3X-RAY DIFFRACTION3C3 - 187
4X-RAY DIFFRACTION4D106 - 147
5X-RAY DIFFRACTION5E3 - 187
6X-RAY DIFFRACTION6F106 - 147

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