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- PDB-5gw6: Water-Bridge Mediates Recognition of mRNA Cap in eIF4E -

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Basic information

Entry
Database: PDB / ID: 5gw6
TitleWater-Bridge Mediates Recognition of mRNA Cap in eIF4E
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / Cap-dependent / Cap-free
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 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleus / 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 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBrown, C.J.
CitationJournal: Structure / Year: 2017
Title: Water-Bridge Mediates Recognition of mRNA Cap in eIF4E
Authors: Lama, D. / Pradhan, M.R. / Brown, C.J. / Eapen, R.S. / Joseph, T.L. / Kwoh, C.K. / Lane, D.P. / Verma, C.S.
History
DepositionSep 8, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 19, 2016ID: 5ABI
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9804
Polymers22,7041
Non-polymers2763
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.695, 128.024, 38.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-501-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 4E / EIF4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 22703.631 Da / Num. of mol.: 1 / Mutation: E105A, K106A, K108A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06730
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3 Å3/Da / Density % sol: 58.98 % / Description: Long needle
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 5000 MME, 100MM TRIS BIS PH 5.0, 0.05M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2015
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→20 Å / Num. obs: 21660 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W97

2w97


Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.374 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22758 1105 5.1 %RANDOM
Rwork0.19673 ---
obs0.19833 20519 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å2-0 Å2
2---0.47 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 18 101 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191550
X-RAY DIFFRACTIONr_bond_other_d0.0030.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9312095
X-RAY DIFFRACTIONr_angle_other_deg0.98533330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14523.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52615262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3041512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it1.8261.803726
X-RAY DIFFRACTIONr_mcbond_other1.8261.802725
X-RAY DIFFRACTIONr_mcangle_it2.952.687904
X-RAY DIFFRACTIONr_mcangle_other2.9492.687905
X-RAY DIFFRACTIONr_scbond_it2.6042.188822
X-RAY DIFFRACTIONr_scbond_other2.5972.188822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1423.1471191
X-RAY DIFFRACTIONr_long_range_B_refined6.46615.6991846
X-RAY DIFFRACTIONr_long_range_B_other6.46315.6991846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 69 -
Rwork0.191 1489 -
obs--97.31 %

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