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- PDB-5t48: Crystal structure of the D. melanogaster eIF4E-eIF4G complex with... -

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Basic information

Entry
Database: PDB / ID: 5t48
TitleCrystal structure of the D. melanogaster eIF4E-eIF4G complex without lateral contact
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 / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / 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 / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / 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 / translational initiation / P-body / neuromuscular junction / mitotic cell cycle / nuclear body / translation / mRNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
: / Translation initiation factor eIF4G-like, eIF4E-binding domain / Initiation factor 4G / 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 ...: / Translation initiation factor eIF4G-like, eIF4E-binding domain / Initiation factor 4G / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / 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: 2.19 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1983
Polymers28,6592
Non-polymers5381
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-13 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.622, 66.196, 75.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 1
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.: 1
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-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TrisHCl pH 8.0, 0.01 M ZnCl2, 20% w/v PEG6000

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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: 2.19→45.62 Å / Num. obs: 12336 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 46.84 Å2 / CC1/2: 0.999 / Rsym value: 0.081 / Net I/σ(I): 17
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.85 / Rsym value: 1.066 / % possible all: 99.6

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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: 2.19→39.063 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.16 / Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2305 637 5.19 %
Rwork0.2085 --
obs0.2096 12278 99.82 %
all-11641 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.66 Å2
Refinement stepCycle: LAST / Resolution: 2.19→39.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 33 35 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031864
X-RAY DIFFRACTIONf_angle_d0.4782528
X-RAY DIFFRACTIONf_dihedral_angle_d12.7921123
X-RAY DIFFRACTIONf_chiral_restr0.038264
X-RAY DIFFRACTIONf_plane_restr0.002333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1901-2.35920.32771320.26822259X-RAY DIFFRACTION99
2.3592-2.59650.26871180.24032288X-RAY DIFFRACTION100
2.5965-2.97210.26531360.23252299X-RAY DIFFRACTION100
2.9721-3.74410.23521240.21632330X-RAY DIFFRACTION100
3.7441-39.06940.20041270.18642465X-RAY DIFFRACTION100
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)
13.94863.0268-3.2147.0167-3.48655.811-0.135-0.1704-0.3468-0.5951-0.3416-0.6990.46030.57130.53670.46870.13220.02020.4680.01270.4619-0.5724-16.185223.8244
23.80220.9663-0.00324.19120.1056.1233-0.06630.49990.1984-0.6504-0.03950.5003-0.0152-0.47020.09030.4210.0395-0.02350.45740.01030.4056-12.0397-11.284519.6472
38.3106-3.82683.02575.0443-2.16185.8317-0.52571.6082.2087-0.776-0.00470.0131-0.2466-0.59450.40210.97360.1016-0.15891.21350.13420.8064-12.1671-6.84464.1385
46.7957-0.9799-1.06826.55666.55378.5634-0.5259-0.3276-0.4988-0.72390.0581-0.3468-0.4545-0.17760.25840.6708-0.05850.15040.37910.06670.5269-18.7657-30.150537.5559
52.7671-1.6736-2.89223.3710.02935.6353-0.4731-0.04690.01061.11110.04960.91070.1081-0.73620.19410.675-0.12250.15690.4715-0.10550.5625-16.697-21.191334.2201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 66 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 597 through 617 )
5X-RAY DIFFRACTION5chain 'B' and (resid 618 through 632 )

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