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- PDB-8uh1: Crystal structure of T. brucei EIF4E6 in complex with EIF4G5 peptide -

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Basic information

Entry
Database: PDB / ID: 8uh1
TitleCrystal structure of T. brucei EIF4E6 in complex with EIF4G5 peptide
Components
  • Eukaryotic translation initiation factor 4E type 6
  • MIF4G domain-containing protein
KeywordsTRANSLATION / Translation initiation factor / eIF4E family / EIF4E6 / EIF4G5
Function / homology
Function and homology information


RNA cap 4 binding / motile cilium assembly / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / post-transcriptional regulation of gene expression / translation initiation factor activity / cell motility / mRNA binding / cytoplasm
Similarity search - Function
Initiation factor 4G / 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
Eukaryotic translation initiation factor 4E type 6 / MIF4G domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsGuimaraes, B.G. / Penteado, R.F.
Funding support France, Brazil, 3items
OrganizationGrant numberCountry
Pasteur InstituteACIP grant PTR 190 France
Brazilian National Council for Scientific and Technological Development (CNPq)442323/2019-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)305095/2021-8 Brazil
CitationJournal: Sci Rep / Year: 2024
Title: Structural analysis of the Trypanosoma brucei EIF4E6/EIF4G5 complex reveals details of the interaction between unusual eIF4F subunits.
Authors: Ferras Penteado, R. / Santana da Silva, R. / Nascimento Moura, D.M. / Barbosa de Lima, G. / Muniz Malvezzi, A. / Tamara da Silva Monteiro, T. / Cavalcanti Xavier, C. / Vichier-Guerre, S. / ...Authors: Ferras Penteado, R. / Santana da Silva, R. / Nascimento Moura, D.M. / Barbosa de Lima, G. / Muniz Malvezzi, A. / Tamara da Silva Monteiro, T. / Cavalcanti Xavier, C. / Vichier-Guerre, S. / Dugue, L. / Pochet, S. / Tonin Zanchin, N.I. / de Souza Reis, C.R. / Pompilio de Melo Neto, O. / Gomes Guimaraes, B.
History
DepositionOct 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: 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 6
B: MIF4G domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,5702
Polymers26,5702
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-25 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.503, 131.185, 59.659
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

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


Mass: 21800.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57V43
#2: Protein/peptide MIF4G domain-containing protein


Mass: 4769.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57VY5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: Complex at 12 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 33% Precipitant Mix 4, 0.09 M NPS, 0.12 M Ethylene ...Details: Complex at 12 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 33% Precipitant Mix 4, 0.09 M NPS, 0.12 M Ethylene glycols, 0.1 M Buffer System 3 (pH 8.5), from Morpheus Screen mixes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.9→44 Å / Num. obs: 16430 / % possible obs: 95.1 % / Redundancy: 13.3 % / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 822 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.898→44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1102 -RANDOM
Rwork0.1923 ---
obs0.1942 16430 79.2 %-
Displacement parametersBiso mean: 37.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.1333 Å20 Å20 Å2
2---0.1485 Å20 Å2
3----0.9848 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.898→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 0 120 1677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081605HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.92193HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d524SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1605HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion210SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1290SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion14.67
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.321 20 -
Rwork0.2467 --
obs0.2506 329 31.55 %
Refinement TLS params.

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)
12.4480.9528-0.86843.6043-1.67467.7540.1644-0.00730.6551-0.0073-0.02380.43490.65510.4349-0.1406-0.03020.0377-0.0444-0.0569-0.0328-0.0902-1.2484-16.95291.9718
21.52270.5643-0.29595.3058-0.6715.12840.0802-0.34680.6547-0.3468-0.0004-0.5410.6547-0.541-0.0798-0.021-0.0737-0.0449-0.0581-0.0138-0.093-13.6698-17.4406-3.5908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B79 - 118
2X-RAY DIFFRACTION2{ A|* }A7 - 178

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