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- PDB-4uea: Complex of D. melanogaster eIF4E with a designed 4E-binding prote... -

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Basic information

Entry
Database: PDB / ID: 4uea
TitleComplex of D. melanogaster eIF4E with a designed 4E-binding protein (Form I)
Components
  • DESIGNED 4E-BP
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN / TRANSLATIONAL REPRESSION
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 / mTORC1-mediated signalling / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation ...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 / mTORC1-mediated signalling / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / muscle cell postsynaptic specialization / trans-synaptic signaling / neuronal ribonucleoprotein granule / RNA metabolic process / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translational initiation / translation initiation factor activity / P-body / neuromuscular junction / postsynapse / nuclear body / translation / cytosol / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E1
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2015
Title: Molecular Architecture of 4E-BP Translational Inhibitors Bound to Eif4E.
Authors: Peter, D. / Igreja, C. / Weber, R. / Wohlbold, L. / Weiler, C. / Ebertsch, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionDec 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Atomic model / Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: DESIGNED 4E-BP
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: DESIGNED 4E-BP
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: DESIGNED 4E-BP


Theoretical massNumber of molelcules
Total (without water)79,0596
Polymers79,0596
Non-polymers00
Water0
1
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: DESIGNED 4E-BP


Theoretical massNumber of molelcules
Total (without water)26,3532
Polymers26,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-15 kcal/mol
Surface area10680 Å2
MethodPISA
2
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: DESIGNED 4E-BP


Theoretical massNumber of molelcules
Total (without water)26,3532
Polymers26,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-14.7 kcal/mol
Surface area10760 Å2
MethodPISA
3
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: DESIGNED 4E-BP


Theoretical massNumber of molelcules
Total (without water)26,3532
Polymers26,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-13.7 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.540, 94.540, 131.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 21249.037 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 80-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein/peptide DESIGNED 4E-BP


Mass: 5103.927 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAIN A, C, E REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, ...THE FIRST FOUR RESIDUES OF CHAIN A, C, E REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE NUMBERS OF CHAIN A, C, E ARE SHIFTE BY -11 RESIDUES. NUMBERING CORRESPONDS TO UNP P48598-2 AND PDB 4AXG. MANUALLY DESIGNED 4E-BP SEQUENCE. THE FIRST SIX AND THE LAST TWO RESIDUES OF CHAIN B, D, F REMAIN FROM THE EXPRESSION VECTOR.

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5
Details: 0.03M EACH DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 0.1M BICINE/TRIZMA BASE PH 8.5, 10% PEG8000, 20% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→47.3 Å / Num. obs: 20025 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 63.49 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.85 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UE8 CHAIN A

4ue8


Resolution: 2.62→47.27 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 31.3 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 68, 218, 219, 220, 222, 223, 224, 236. CHAIN B, ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 68, 218, 219, 220, 222, 223, 224, 236. CHAIN B, RESIDUE 0. CHAIN C, RESIDUES 152, 190, 227. CHAIN E, RESIDUES 222, 223. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 237 TO 248. CHAIN C, RESIDUES 236 TO 248. CHAIN E, RESIDUES 235 TO 248.
RfactorNum. reflection% reflection
Rfree0.2616 1013 5.1 %
Rwork0.2052 --
obs0.2081 19990 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.1 Å2
Refinement stepCycle: LAST / Resolution: 2.62→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5001 0 0 0 5001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035115
X-RAY DIFFRACTIONf_angle_d0.6476927
X-RAY DIFFRACTIONf_dihedral_angle_d12.6471890
X-RAY DIFFRACTIONf_chiral_restr0.025742
X-RAY DIFFRACTIONf_plane_restr0.002884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6201-2.75830.35031150.28042693X-RAY DIFFRACTION99
2.7583-2.93110.34561220.2682727X-RAY DIFFRACTION99
2.9311-3.15730.33691420.25812717X-RAY DIFFRACTION99
3.1573-3.4750.32421740.23832667X-RAY DIFFRACTION100
3.475-3.97760.27671350.2142726X-RAY DIFFRACTION100
3.9776-5.01040.22611640.17532718X-RAY DIFFRACTION100
5.0104-47.27770.22091610.17782729X-RAY DIFFRACTION99

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