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

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Basic information

Entry
Database: PDB / ID: 4ueb
TitleComplex of D. melanogaster eIF4E with a designed 4E-binding protein (Form II)
Components
  • DESIGNED 4E-BP
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
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 / 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 / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / translational initiation / P-body / neuromuscular junction / 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: 2.52 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 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Dec 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
Water18010
1
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: DESIGNED 4E-BP


Theoretical massNumber of molelcules
Total (without water)26,3532
Polymers26,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-15.6 kcal/mol
Surface area10850 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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-15.2 kcal/mol
Surface area10410 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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-13.1 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 94.530, 167.370
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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES PH 6.5, 22% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.52→47.9 Å / Num. obs: 20795 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 43.75 Å2 / Rsym value: 0.11 / Net I/σ(I): 9.4
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 97.1

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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: 2.52→41.843 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 24.87 / 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 67, 152, 177, 190, 215. CHAIN B, RESIDUE -2. CHAIN ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 67, 152, 177, 190, 215. CHAIN B, RESIDUE -2. CHAIN C, RESIDUES 190, 222, 235. CHAIN D, RESIDUE -2. CHAIN E, RESIDUES 151, 152, 190. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 219 TO 224 AND 235 TO 248. CHAIN C, RESIDUES 236 TO 248. CHAIN E, RESIDUES 236 TO 244.
RfactorNum. reflection% reflection
Rfree0.245 1058 5.1 %
Rwork0.2045 --
obs0.2065 20794 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 2.52→41.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5044 0 0 10 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045157
X-RAY DIFFRACTIONf_angle_d0.6716987
X-RAY DIFFRACTIONf_dihedral_angle_d11.6681901
X-RAY DIFFRACTIONf_chiral_restr0.027753
X-RAY DIFFRACTIONf_plane_restr0.002891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.63470.36761280.27172459X-RAY DIFFRACTION97
2.6347-2.77360.29671260.23732497X-RAY DIFFRACTION98
2.7736-2.94730.30871320.23232421X-RAY DIFFRACTION97
2.9473-3.17480.25831550.21562434X-RAY DIFFRACTION97
3.1748-3.49410.28341250.20842499X-RAY DIFFRACTION97
3.4941-3.99940.20261120.18572437X-RAY DIFFRACTION96
3.9994-5.03740.20251360.18412448X-RAY DIFFRACTION94
5.0374-41.84820.22811440.19932541X-RAY DIFFRACTION93

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