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- PDB-4uec: Complex of D. melanogaster eIF4E with eIF4G and cap analog -

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Basic information

Entry
Database: PDB / ID: 4uec
TitleComplex of D. melanogaster eIF4E with eIF4G and cap analog
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4G, ISOFORM A
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN / TRANSLATION INITIATION
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 / neuronal ribonucleoprotein granule / RNA metabolic process / 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
7N-METHYL-8-HYDROGUANOSINE-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: 2.4 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX 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
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4475
Polymers51,3693
Non-polymers1,0782
Water79344
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4G, ISOFORM A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,1202
Non-polymers5391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-14.2 kcal/mol
Surface area11380 Å2
MethodPISA
2
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,2491
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 68.070, 103.880
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.: 2 / 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 EUKARYOTIC TRANSLATION INITIATION FACTOR 4G, ISOFORM A / EUKARYOTIC TRANSLATION INITIATION FACTOR 4G / ISOFORM C / FI02056P / TRANSLATION INITIATION FACTOR EIF4G


Mass: 8870.968 Da / Num. of mol.: 1 / Fragment: RESIDUES 578-650
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: O61380
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAIN A AND CHAIN C REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP ...THE FIRST FOUR RESIDUES OF CHAIN A AND CHAIN C REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE NUMBERS OF CHAIN A ARE SHIFTED BY -11 RESIDUES. NUMBERING CORRESPONDS TO UNP P48598-2 AND PDB 4AXG. THE FIRST FIVE RESIDUES OF CHAIN B REMAIN FROM THE EXPRESSION TAG.

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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: 45 % / Description: NONE
Crystal growpH: 6 / Details: 0.1M MES PH 6.0, 20% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.038
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2.4→48.6 Å / Num. obs: 15790 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 42.42 Å2 / Rsym value: 0.1 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.79 / % possible all: 99.8

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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: 2.4→48.545 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 27.22 / 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 151, 152. CHAIN B, RESIDUES 602, 603, 607, 613, ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 151, 152. CHAIN B, RESIDUES 602, 603, 607, 613, 614, 636. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 237 TO 248. CHAIN B, RESIDUES 578 TO 601 AND 638 TO 650. CHAIN C, RESIDUES 237 TO 248.
RfactorNum. reflection% reflection
Rfree0.2532 840 5.3 %
Rwork0.2095 --
obs0.2119 15777 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 66 44 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033209
X-RAY DIFFRACTIONf_angle_d0.6674361
X-RAY DIFFRACTIONf_dihedral_angle_d12.4791185
X-RAY DIFFRACTIONf_chiral_restr0.028459
X-RAY DIFFRACTIONf_plane_restr0.002544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55040.30091370.26512422X-RAY DIFFRACTION100
2.5504-2.74730.36641550.26252438X-RAY DIFFRACTION100
2.7473-3.02370.25911300.2492460X-RAY DIFFRACTION100
3.0237-3.46110.25021350.22882479X-RAY DIFFRACTION100
3.4611-4.36020.26391460.18362503X-RAY DIFFRACTION100
4.3602-48.55520.20391370.18662635X-RAY DIFFRACTION100

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