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- PDB-5me5: Crystal Structure of eiF4E from C. melo bound to a eIF4G peptide -

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Basic information

Entry
Database: PDB / ID: 5me5
TitleCrystal Structure of eiF4E from C. melo bound to a eIF4G peptide
Components
  • Eukaryotic transcription initiation factor 4E
  • eIF4G
KeywordsTRANSLATION / translation initiation eIF4F complex
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translational initiation / translation initiation factor activity / defense response to virus / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / Initiation factor eIF-4 gamma, MA3 / MA3 domain ...: / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
eukaryotic translation initiation factor 4G-like isoform X1 / Eukaryotic translation initiation factor 4E-1
Similarity search - Component
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsQuerol-Audi, J. / Silva, C. / Miras, M. / Truniger, V. / Aranda-Regules, M. / Verdaguer, N.
CitationJournal: Plant Physiol. / Year: 2017
Title: Structure of eIF4E in Complex with an eIF4G Peptide Supports a Universal Bipartite Binding Mode for Protein Translation.
Authors: Miras, M. / Truniger, V. / Silva, C. / Verdaguer, N. / Aranda, M.A. / Querol-Audi, J.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: 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 transcription initiation factor 4E
B: eIF4G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7274
Polymers36,5352
Non-polymers1922
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-47 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.094, 70.352, 42.798
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic transcription initiation factor 4E / Eukaryotic translation initiation factor 4E


Mass: 26744.484 Da / Num. of mol.: 1 / Fragment: eIF4e
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: Q00LS8
#2: Protein eIF4G


Mass: 9790.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A1S3C4H6*PLUS
#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.: 61 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.5 / Details: ammonium sulphate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.981
ReflectionResolution: 1.9→42.713 Å / Num. obs: 17809 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.079 / Net I/av σ(I): 8.688 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-23.30.6081.3199.7
2-2.123.90.4171.81100
2.12-2.273.80.2912.6199.9
2.27-2.453.80.1993.8199.8
2.45-2.693.80.145.4199.8
2.69-33.80.098.2199.9
3-3.473.80.05513.11100
3.47-4.253.90.03618.6199.9
4.25-6.013.80.03417.91100
6.01-29.3323.70.03119.8199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
SCALA3.3.21data scaling
XDSdata reduction
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.332 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2135 872 4.9 %
Rwork0.1864 --
obs0.1877 17788 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 10 61 1610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061597
X-RAY DIFFRACTIONf_angle_d0.7572168
X-RAY DIFFRACTIONf_dihedral_angle_d3.11914
X-RAY DIFFRACTIONf_chiral_restr0.052220
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.0190.30031450.23772790X-RAY DIFFRACTION100
2.019-2.17490.24151490.20452795X-RAY DIFFRACTION100
2.1749-2.39360.22821610.19292815X-RAY DIFFRACTION100
2.3936-2.73980.2271390.17742813X-RAY DIFFRACTION100
2.7398-3.4510.21271380.17582838X-RAY DIFFRACTION100
3.451-29.33530.18431400.18142865X-RAY DIFFRACTION100

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