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- PDB-3m93: Complex crystal structure of Ascaris suum eIF4E-3 with m7G cap -

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Basic information

Entry
Database: PDB / ID: 3m93
TitleComplex crystal structure of Ascaris suum eIF4E-3 with m7G cap
Components
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Translation initiation factor 4E
KeywordsTRANSLATION / eIF4E / Berkeley Structural Genomics Center / BSGC
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 / RNA 7-methylguanosine cap binding / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / positive regulation of mitotic cell cycle ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA 7-methylguanosine cap binding / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor 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 / 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
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 4E-binding protein 1 / eIF-4F 25 kDa subunit
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, W. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation.
Authors: Liu, W. / Jankowska-Anyszka, M. / Piecyk, K. / Dickson, L. / Wallace, A. / Niedzwiecka, A. / Stepinski, J. / Stolarski, R. / Darzynkiewicz, E. / Kieft, J. / Zhao, R. / Jones, D.N. / Davis, R.E.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 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
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,3142
Non-polymers4581
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.620, 104.620, 47.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Details1

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Components

#1: Protein Translation initiation factor 4E


Mass: 22169.328 Da / Num. of mol.: 1 / Fragment: UNP residues 49-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Strain: pig roundworm / Gene: Ascaris suum / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q6PKX2
#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: 2144.564 Da / Num. of mol.: 1 / Fragment: UNP residues 51-67 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: 20% MMG PEG 2000, 0.2 M (NH4)2SO4, and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 10, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→36.99 Å / Num. obs: 5719 / % possible obs: 98.5 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113
Reflection shellResolution: 2.9→2.974 Å

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASESphasing
REFMAC5.5.0072refinement
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8W

2v8w


Resolution: 2.9→14.92 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.861 / SU B: 21.211 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 1.8 / σ(I): 2.9 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29372 550 9.7 %RANDOM
Rwork0.23934 ---
all0.298 5719 --
obs0.24469 5122 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.926 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2---2 Å20 Å2
3---4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 29 2 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9542202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06223.71878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15515247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4671511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211235
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5511.5958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03521527
X-RAY DIFFRACTIONr_scbond_it1.0453654
X-RAY DIFFRACTIONr_scangle_it1.774.5675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 30 -
Rwork0.357 374 -
obs--98.3 %

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