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- PDB-6fc1: Crystal structure of the eIF4E-Eap1p complex from Saccharomyces c... -

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Basic information

Entry
Database: PDB / ID: 6fc1
TitleCrystal structure of the eIF4E-Eap1p complex from Saccharomyces cerevisiae in the cap-bound state
Components
  • Eukaryotic translation initiation factor 4EEIF4E
  • Protein EAP1
KeywordsTRANSLATION / Gene expression Translation Translation initiation Translational control
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / : / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / : / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / cytoplasmic stress granule / negative regulation of translation / regulation of cell cycle / ribosome / mRNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
eIF4E-associated protein / eIF4E-associated protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E / Protein EAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
B: Protein EAP1
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,45512
Polymers58,8264
Non-polymers1,6298
Water9,260514
1
A: Eukaryotic translation initiation factor 4E
B: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1365
Polymers29,4132
Non-polymers7223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-33 kcal/mol
Surface area12680 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3207
Polymers29,4132
Non-polymers9075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-33 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.712, 121.726, 62.348
Angle α, β, γ (deg.)90.00, 132.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Eukaryotic translation initiation factor 4E / EIF4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 21822.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CDC33, TIF45, YOL139C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07260
#2: Protein Protein EAP1 / eIF4E-associated protein 1


Mass: 7590.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: EAP1, YKL204W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36041
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MIB (sodium malonate:imidazole:boric acid in molar ratios of 2:3:3) buffer (pH 7.0) 21% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.35→46.32 Å / Num. obs: 108809 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rsym value: 0.045 / Net I/σ(I): 16.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.6 % / Num. measured obs: 33379 / Num. unique obs: 5058 / CC1/2: 0.643 / Rsym value: 1.284 / % possible all: 92.6

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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: 1.35→46.317 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1683 5391 4.96 %
Rwork0.1377 --
obs0.1392 108796 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→46.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 102 514 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124196
X-RAY DIFFRACTIONf_angle_d1.2795727
X-RAY DIFFRACTIONf_dihedral_angle_d17.4721583
X-RAY DIFFRACTIONf_chiral_restr0.114607
X-RAY DIFFRACTIONf_plane_restr0.009744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36540.3611840.31863243X-RAY DIFFRACTION92
1.3654-1.38140.33031600.29873288X-RAY DIFFRACTION94
1.3814-1.39830.3771680.27773262X-RAY DIFFRACTION94
1.3983-1.4160.27221760.24693352X-RAY DIFFRACTION94
1.416-1.43460.27641860.22043314X-RAY DIFFRACTION95
1.4346-1.45430.24941620.20583384X-RAY DIFFRACTION96
1.4543-1.4750.24451900.17773360X-RAY DIFFRACTION97
1.475-1.49710.18941760.1563392X-RAY DIFFRACTION97
1.4971-1.52050.20071680.13633435X-RAY DIFFRACTION97
1.5205-1.54540.17891630.13373346X-RAY DIFFRACTION96
1.5454-1.5720.1711540.13163451X-RAY DIFFRACTION98
1.572-1.60060.19061750.13193472X-RAY DIFFRACTION98
1.6006-1.63140.17141810.12613451X-RAY DIFFRACTION98
1.6314-1.66470.16741660.12783498X-RAY DIFFRACTION99
1.6647-1.70090.18731810.12893479X-RAY DIFFRACTION99
1.7009-1.74050.17441870.12763480X-RAY DIFFRACTION99
1.7405-1.7840.16422040.1193468X-RAY DIFFRACTION99
1.784-1.83220.16491770.11733512X-RAY DIFFRACTION100
1.8322-1.88620.16192090.11573462X-RAY DIFFRACTION100
1.8862-1.9470.15171780.11773527X-RAY DIFFRACTION100
1.947-2.01660.16161910.12143496X-RAY DIFFRACTION100
2.0166-2.09740.14212030.11613476X-RAY DIFFRACTION100
2.0974-2.19280.1461940.11673506X-RAY DIFFRACTION100
2.1928-2.30840.14841710.12023543X-RAY DIFFRACTION100
2.3084-2.4530.18231770.12883517X-RAY DIFFRACTION100
2.453-2.64240.14692010.13143509X-RAY DIFFRACTION100
2.6424-2.90830.15941720.13243523X-RAY DIFFRACTION100
2.9083-3.32910.15491800.1343546X-RAY DIFFRACTION100
3.3291-4.19380.14791690.1273542X-RAY DIFFRACTION100
4.1938-46.34420.18231880.16583571X-RAY DIFFRACTION100

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