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- PDB-6o7y: Trypanosoma cruzi EIF4E5 translation initiation factor in complex... -

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Basic information

Entry
Database: PDB / ID: 6o7y
TitleTrypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-4
ComponentsPutative Eukaryotic translation initiation factor 4E type 5
KeywordsRNA BINDING PROTEIN / Translation Initiation Factor / trypanosomatids / cap-4
Function / homologyTranslation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / Chem-LRM / Putative Eukaryotic translation initiation factor 4E type 5
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuimaraes, B.G. / Reolon, L.W.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4.
Authors: Reolon, L.W. / Vichier-Guerre, S. / de Matos, B.M. / Dugue, L. / Assuncao, T.R.D.S. / Zanchin, N.I.T. / Pochet, S. / Guimaraes, B.G.
History
DepositionMar 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2874
Polymers25,2691
Non-polymers2,0183
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.590, 102.590, 41.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 25268.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_13g194 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2VRR6
#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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BisTris pH 6.5, 30% PEG3350, 0.2M Lithium Sulfate, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9586 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9586 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12900 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 81.08 Å2 / CC1/2: 1 / Net I/σ(I): 23.7
Reflection shellResolution: 2.2→2.33 Å / Num. unique obs: 2040 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.963 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.226 643 4.99 %RANDOM
Rwork0.207 ---
obs0.208 12873 99.9 %-
Displacement parametersBiso mean: 93.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.9141 Å20 Å20 Å2
2---0.9141 Å20 Å2
3---1.8283 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.2→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 130 68 1650
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011628HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152241HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes318HARMONIC5
X-RAY DIFFRACTIONt_it1628HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion18.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion209SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1895SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.41 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2266 151 4.98 %
Rwork0.2196 2884 -
all0.22 3035 -
obs--99.64 %
Refinement TLS params.Method: refined / Origin x: -33.0662 Å / Origin y: -24.1599 Å / Origin z: 2.0946 Å
111213212223313233
T-0.2341 Å20.0286 Å20.0062 Å2--0.212 Å20.0681 Å2---0.1562 Å2
L5.1479 °2-3.3565 °2-1.0434 °2-3.8932 °21.4868 °2--2.5559 °2
S-0.032 Å °-0.0696 Å °0.4861 Å °0.2074 Å °0.1146 Å °-0.3478 Å °-0.1162 Å °0.3106 Å °-0.0827 Å °
Refinement TLS groupSelection details: { A|* }

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