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- PDB-9q72: Trypanosoma brucei EIF4E5 translation initiation factor in comple... -

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Basic information

Entry
Database: PDB / ID: 9q72
TitleTrypanosoma brucei EIF4E5 translation initiation factor in complex with cap-4
ComponentsEukaryotic translation initiation factor 4E type 5
KeywordsTRANSLATION / RNA BINDING PROTEIN / TRANSLATION INITIATION FACTOR / TRYPANOSOMATIDS / CAP-4
Function / homology
Function and homology information


RNA cap 4 binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / ciliary plasm / nuclear lumen / translation initiation factor activity / translational initiation / cell motility / translation / cytoplasm
Similarity search - Function
Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like
Similarity search - Domain/homology
IMIDAZOLE / Chem-LRM / Eukaryotic translation initiation factor 4E type 5
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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: To Be Published
Title: Trypanosoma brucei EIF4E5 translation initiation factor in complex with cap-4
Authors: Penteado, R.F. / Guimaraes, B.G.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2437
Polymers24,1781
Non-polymers2,0646
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.660, 72.660, 95.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-206-

MG

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 24178.377 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

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Non-polymers , 6 types, 215 molecules

#2: 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
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein at 7.5 mg/mL, in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization solution containing 0.03 M Divalents, 0.1 M buffer system 1 (pH 6.5), ...Details: Protein at 7.5 mg/mL, in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization solution containing 0.03 M Divalents, 0.1 M buffer system 1 (pH 6.5), 24% precipitant Mix, 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 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.25→37.98 Å / Num. obs: 80904 / % possible obs: 96.1 % / Redundancy: 19.9 % / CC1/2: 0.999 / Net I/σ(I): 23.1
Reflection shellResolution: 1.252→3.563 Å / Num. unique obs: 3729 / CC1/2: 0.615

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.98 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.355 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 4040 5 %RANDOM
Rwork0.13922 ---
obs0.14067 76755 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å2-0 Å2
3----2.98 Å2
Refinement stepCycle: 1 / Resolution: 1.25→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 133 209 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131950
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161764
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.8832736
X-RAY DIFFRACTIONr_angle_other_deg0.6431.8474097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.07659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72310297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02422
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_it7.1642.581824
X-RAY DIFFRACTIONr_mcbond_other7.1262.574822
X-RAY DIFFRACTIONr_mcangle_it10.2245.1991046
X-RAY DIFFRACTIONr_mcangle_other10.2215.2091047
X-RAY DIFFRACTIONr_scbond_it78.6215.0951126
X-RAY DIFFRACTIONr_scbond_other78.5865.0971127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4741676
X-RAY DIFFRACTIONr_long_range_B_refined90.5930.412118
X-RAY DIFFRACTIONr_long_range_B_other90.83526.532049
X-RAY DIFFRACTIONr_rigid_bond_restr20.15933714
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 294 -
Rwork0.393 5588 -
obs--99.43 %
Refinement TLS params.Method: refined / Origin x: 29.0232 Å / Origin y: -12.2588 Å / Origin z: -3.7717 Å
111213212223313233
T0.0522 Å2-0.0167 Å2-0.0037 Å2-0.0087 Å20.0009 Å2--0.0473 Å2
L0.5216 °20.4627 °2-0.4304 °2-0.4691 °2-0.4539 °2--0.8299 °2
S0.013 Å °-0.0285 Å °-0.0416 Å °-0.0005 Å °-0.0276 Å °-0.0071 Å °0.0724 Å °-0.0172 Å °0.0146 Å °

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