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- PDB-5t47: Crystal structure of the D. melanogaster eIF4E-eIF4G complex -

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Basic information

Entry
Database: PDB / ID: 5t47
TitleCrystal structure of the D. melanogaster eIF4E-eIF4G complex
Components
  • Eukaryotic translation initiation factor 4E
  • Eukaryotic translation initiation factor 4G, isoform A
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E-BINDING PROTEIN / TRANSLATION INITIATION / eIF4F
Function / homology
Function and homology information


TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / muscle cell postsynaptic specialization / RNA metabolic process / neuronal ribonucleoprotein granule / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / neuromuscular junction / translational initiation / P-body / mitotic cell cycle / regulation of translation / nuclear body / translation / mRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
: / Translation initiation factor eIF4G-like, eIF4E-binding 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 / eIF4-gamma/eIF5/eIF2-epsilon ...: / Translation initiation factor eIF4G-like, eIF4E-binding 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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / 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 4G1, isoform A / Eukaryotic translation initiation factor 4E1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGruener, S. / Peter, D. / Weber, R. / Wohlbold, L. / Chung, M.-Y. / Weichenrieder, O. / Valkov, E. / Igreja, C. / Izaurralde, E.
CitationJournal: Mol.Cell / Year: 2016
Title: The Structures of eIF4E-eIF4G Complexes Reveal an Extended Interface to Regulate Translation Initiation.
Authors: Gruner, S. / Peter, D. / Weber, R. / Wohlbold, L. / Chung, M.Y. / Weichenrieder, O. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4G, isoform A
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4G, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5036
Polymers57,3194
Non-polymers1842
Water2,828157
1
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4G, isoform A


Theoretical massNumber of molelcules
Total (without water)28,6592
Polymers28,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-19 kcal/mol
Surface area11390 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4G, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8444
Polymers28,6592
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-21 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.295, 49.714, 58.627
Angle α, β, γ (deg.)102.70, 103.94, 116.08
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21249.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: eIF-4E, Eif4e, EIF4F, CG4035 / Plasmid: PETMCN / Details (production host): (PNYC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein Eukaryotic translation initiation factor 4G, isoform A / Eukaryotic translation initiation factor 4G / isoform C / FI02056p / Translation initiation factor eIF4G


Mass: 7410.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: eIF4G, eIF-4G, eIF4G-RA, CG10811, Dmel_CG10811 / Plasmid: PETMCN / Details (production host): (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O61380
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 0.1 M TrisHCl pH 8.25, 0.2 M MgCl2, 32% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.2→41.42 Å / Num. obs: 20740 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.992 / Rsym value: 0.121 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.683 / Rsym value: 0.609 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UE8

4ue8


Resolution: 2.2→41.415 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 29
Details: TORSIONAL NCS RESTRAINTS WERE APPLIED RELATING CHAINS A, B TO CHAINS C, D. HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2338 938 4.53 %
Rwork0.2079 --
obs0.2092 20729 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 12 157 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023705
X-RAY DIFFRACTIONf_angle_d0.4685007
X-RAY DIFFRACTIONf_dihedral_angle_d13.1192230
X-RAY DIFFRACTIONf_chiral_restr0.04533
X-RAY DIFFRACTIONf_plane_restr0.002642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.3160.32731400.29752727X-RAY DIFFRACTION93
2.316-2.46110.29361320.26432821X-RAY DIFFRACTION97
2.4611-2.65110.27011150.23642849X-RAY DIFFRACTION97
2.6511-2.91780.26281290.21682874X-RAY DIFFRACTION97
2.9178-3.33990.26161250.20892855X-RAY DIFFRACTION98
3.3399-4.20720.18051310.17072863X-RAY DIFFRACTION97
4.2072-41.42240.21361660.18912802X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / 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)
11.17570.37610.5822.9369-0.88993.5965-0.0965-0.69540.080.27940.32710.38380.3077-0.7630.77710.6752-0.0658-0.0210.2361-0.08660.06462.6111-26.497214.028
21.13680.63560.54171.903-0.05862.6750.00380.09270.0468-0.1397-0.0527-0.022-0.0621-0.0606-0.01750.54270.0077-0.05860.18070.00240.19169.2822-23.62942.5827
31.36990.311-1.32130.1385-0.53292.24120.1680.69810.2573-0.5861-0.1412-0.1464-0.1220.08460.06940.91160.0509-0.02460.3680.11830.225814.9704-10.5539-3.1447
43.59560.1032-1.09393.5368-0.04534.26550.21190.0532-1.0542-0.1649-0.0601-0.12390.9790.5661-0.13270.74450.1599-0.140.2891-0.01950.44622.8369-42.884214.8789
52.2223-0.1280.50761.45480.22222.19360.25640.2833-0.43540.0961-0.05280.12260.9902-0.3348-0.03510.7876-0.0368-0.07370.32470.00740.29995.7035-38.249910.9099
62.354-1.18170.82131.7252-1.22192.64550.1031-0.2319-0.439-0.12290.1330.23070.62940.0110.02940.5821-0.0224-0.09950.1979-0.00750.223815.0519-30.79732.9401
71.9709-0.3834-0.29212.11990.25622.38650.121-0.13940.01280.04510.0204-0.32610.17630.4859-0.07660.45550.0201-0.07770.2237-0.03480.193225.1121-22.28534.0054
82.05131.60711.00571.48030.09462.6150.10950.50540.33270.0825-0.2896-0.67480.09761.2493-0.21060.53960.00910.01940.7097-0.00250.532638.718-22.577328.8892
92.34680.5020.96271.64642.20013.0351-0.01670.02430.4484-0.1096-0.13730.1369-0.422-0.02370.11210.68190.0949-0.06620.1938-0.02480.26475.7751-5.753425.7719
101.6131-0.39240.31751.37480.14961.69830.1432-0.25420.0352-0.106-0.11590.12240.19590.03630.02650.4921-0.0302-0.03240.1851-0.03150.1788.2145-17.051835.9008
111.9483-0.4949-0.60171.76551.17483.93380.031-0.39560.33580.6766-0.05790.06040.0057-0.3498-0.03270.8017-0.0849-0.02190.3983-0.05230.34669.0874-26.425849.1555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 248 )
4X-RAY DIFFRACTION4chain 'B' and (resid 603 through 617 )
5X-RAY DIFFRACTION5chain 'B' and (resid 618 through 648 )
6X-RAY DIFFRACTION6chain 'C' and (resid 67 through 101 )
7X-RAY DIFFRACTION7chain 'C' and (resid 102 through 230)
8X-RAY DIFFRACTION8chain 'C' and (resid 231 through 248 )
9X-RAY DIFFRACTION9chain 'D' and (resid 601 through 617 )
10X-RAY DIFFRACTION10chain 'D' and (resid 618 through 643 )
11X-RAY DIFFRACTION11chain 'D' and (resid 644 through 656 )

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