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- PDB-6fc0: Crystal structure of the eIF4E-eIF4G complex from Chaetomium ther... -

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Basic information

Entry
Database: PDB / ID: 6fc0
TitleCrystal structure of the eIF4E-eIF4G complex from Chaetomium thermophilum
Components
  • Eukaryotic translation initiation factor 4E-like protein
  • Eukaryotic translation initiation factor 4G
KeywordsTRANSLATION / Translation Translational control Translation initiation Gene expression
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / cytoplasmic stress granule / regulation of translation / mRNA binding
Similarity search - Function
Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / 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 ...Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / 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 / 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 4E-like protein / MIF4G domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.293 Å
AuthorsGruener, S. / Valkov, E.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast.
Authors: Gruner, S. / Weber, R. / Peter, D. / Chung, M.Y. / Igreja, C. / Valkov, E. / Izaurralde, E.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Eukaryotic translation initiation factor 4E-like protein
B: Eukaryotic translation initiation factor 4G


Theoretical massNumber of molelcules
Total (without water)32,1302
Polymers32,1302
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-30 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.587, 75.169, 48.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21A-448-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 4E-like protein


Mass: 23081.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0058450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SCU4
#2: Protein Eukaryotic translation initiation factor 4G


Mass: 9048.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0071550 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SFP0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 1.8 Å3/Da / Density % sol: 31.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20000 20% PEG 500 MME 0.03 M diethyleneglycol 0.03 M triethyleneglycol 0.03 M tetraethyleneglycol 0.03 M pentaethyleneglycol 0.1 M Bicine/Trizma pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→40.71 Å / Num. obs: 54870 / % possible obs: 93.9 % / Redundancy: 3.1 % / Rsym value: 0.048 / Net I/σ(I): 11.5
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7178 / CC1/2: 0.584 / Rsym value: 0.713 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBZ, chain A

6fbz


Resolution: 1.293→40.71 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.96
RfactorNum. reflection% reflection
Rfree0.2009 2744 5 %
Rwork0.1634 --
obs0.1654 54840 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.293→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 230 2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082306
X-RAY DIFFRACTIONf_angle_d0.9413136
X-RAY DIFFRACTIONf_dihedral_angle_d16.239881
X-RAY DIFFRACTIONf_chiral_restr0.075331
X-RAY DIFFRACTIONf_plane_restr0.007410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2933-1.31560.26611080.24392049X-RAY DIFFRACTION74
1.3156-1.33950.28681290.23782461X-RAY DIFFRACTION90
1.3395-1.36530.27681310.24092478X-RAY DIFFRACTION90
1.3653-1.39310.24241330.22532538X-RAY DIFFRACTION91
1.3931-1.42340.32351340.22312536X-RAY DIFFRACTION92
1.4234-1.45660.26451330.22552524X-RAY DIFFRACTION93
1.4566-1.4930.24621330.20632538X-RAY DIFFRACTION92
1.493-1.53340.24831370.18652598X-RAY DIFFRACTION94
1.5334-1.57850.23811370.17262597X-RAY DIFFRACTION95
1.5785-1.62940.21811390.16862650X-RAY DIFFRACTION95
1.6294-1.68770.22291420.15472685X-RAY DIFFRACTION96
1.6877-1.75520.17561400.14782669X-RAY DIFFRACTION96
1.7552-1.83510.20211400.14852663X-RAY DIFFRACTION96
1.8351-1.93190.16491440.13982722X-RAY DIFFRACTION97
1.9319-2.05290.1721430.13752711X-RAY DIFFRACTION98
2.0529-2.21140.16581420.14052711X-RAY DIFFRACTION97
2.2114-2.43390.17311430.14362720X-RAY DIFFRACTION96
2.4339-2.7860.17841410.15452674X-RAY DIFFRACTION95
2.786-3.50980.19841450.16412741X-RAY DIFFRACTION96
3.5098-40.73030.21271500.16912831X-RAY DIFFRACTION94

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