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- PDB-3hxi: Crystal structure of Schistosome eIF4E complexed with m7GpppG and... -

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Basic information

Entry
Database: PDB / ID: 3hxi
TitleCrystal structure of Schistosome eIF4E complexed with m7GpppG and 4E-BP
Components
  • Eukaryotic Translation Initiation 4E
  • 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 / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / 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 / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / 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: 1.8 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 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4743
Polymers24,6712
Non-polymers8031
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-9 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.311, 125.330, 37.330
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 4E


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: pGEX6p-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-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 277 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 277K

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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: 1.8→24 Å / Num. obs: 22977 / Redundancy: 4 %

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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: 1.8→24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.461 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27158 1969 10.2 %RANDOM
Rwork0.21831 ---
obs0.22355 17407 94.46 %-
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: 23.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---1 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 52 112 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9862386
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59823.52388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81515295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0681515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2799
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21175
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0031.51026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52321610
X-RAY DIFFRACTIONr_scbond_it2.173879
X-RAY DIFFRACTIONr_scangle_it3.3284.5771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 139 -
Rwork0.28 1314 -
obs--97.39 %

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