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- PDB-3hxg: Crystal structure of Schistsome eIF4E complexed with m7GpppA and 4E-BP -

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Basic information

Entry
Database: PDB / ID: 3hxg
TitleCrystal structure of Schistsome eIF4E complexed with m7GpppA and 4E-BP
Components
  • Eukaryotic Translation Initiation Factor 4EEIF4E
  • Eukaryotic translation initiation factor 4E-binding protein 1
KeywordsTRANSLATION / protein-mRNA cap complex / Acetylation / Phosphoprotein / Protein synthesis inhibitor / Translation regulation
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / TOR signaling / mTORC1-mediated signalling / translation initiation factor binding / negative regulation of translational initiation / translation repressor activity / positive regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / negative regulation of translation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / TOR signaling / mTORC1-mediated signalling / translation initiation factor binding / negative regulation of translational initiation / translation repressor activity / positive regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / negative regulation of translation / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GTA / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, W. / Zhao, R. / Jones, D.N.M. / Davis, R.E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural insights into parasite EIF4E binding specificity for m7G and m2,2,7G mRNA cap.
Authors: Liu, W. / Zhao, R. / McFarland, C. / Kieft, J. / Niedzwiecka, A. / Jankowska-Anyszka, M. / Stepinski, J. / Darzynkiewicz, E. / Jones, D.N. / Davis, R.E.
History
DepositionJun 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic Translation Initiation Factor 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4583
Polymers24,6712
Non-polymers7871
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.560, 125.400, 37.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Eukaryotic Translation Initiation Factor 4E / EIF4E


Mass: 22237.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: eif4e / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90
#2: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by ...eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 2432.823 Da / Num. of mol.: 1 / Fragment: residues 51-67 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical ChemComp-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM pH 6.5 Mops, 20% PEG4K, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.5 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.1→32.08 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.113

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v8w

2v8w


Resolution: 2.1→32 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.416 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1296 9.9 %RANDOM
Rwork0.20971 ---
obs0.2155 11767 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 51 114 1783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9832344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2192485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47915277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6251512
X-RAY DIFFRACTIONr_chiral_restr0.080.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021310
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.2750
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21161
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.51030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3721599
X-RAY DIFFRACTIONr_scbond_it2.0913844
X-RAY DIFFRACTIONr_scangle_it3.1154.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 106 -
Rwork0.227 835 -
obs--99.89 %

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