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- PDB-1l8b: Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (... -

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Basic information

Entry
Database: PDB / ID: 1l8b
TitleCocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to 7-methylGpppG
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
KeywordsRNA BINDING PROTEIN / eukaryotic initiation factor 4E / eIF4E / cap / 7-methylGpppG
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / mTORC1-mediated signalling / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / : / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsNiedzwiecka, A. / Marcotrigiano, J. / Stepinski, J. / Jankowska-Anyszka, M. / Wyslouch-Cieszynska, A. / Dadlez, M. / Gingras, A.-C. / Mak, P. / Darzynkiewicz, E. / Sonenberg, N.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5' cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins.
Authors: Niedzwiecka, A. / Marcotrigiano, J. / Stepinski, J. / Jankowska-Anyszka, M. / Wyslouch-Cieszynska, A. / Dadlez, M. / Gingras, A.C. / Mak, P. / Darzynkiewicz, E. / Sonenberg, N. / Burley, S.K. / Stolarski, R.
History
DepositionMar 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Category: citation_author / struct_site
Item: _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN THE 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE (MGP) IS ACTUALLY BOUND TO ANOTHER GUANOSINE-5'- ...HETEROGEN THE 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE (MGP) IS ACTUALLY BOUND TO ANOTHER GUANOSINE-5'-MONOPHOSPHATE, WHICH IS MISSING IN THE ELECTRON DENSITY.

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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 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3674
Polymers44,2902
Non-polymers1,0762
Water3,351186
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6832
Polymers22,1451
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6832
Polymers22,1451
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.12, 75.92, 77.84
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E / EIF-4E / EIF4E / MRNA CAP-BINDING PROTEIN / EIF-4F 25 KDA SUBUNIT


Mass: 22145.113 Da / Num. of mol.: 2 / Fragment: residues 28-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63073
#2: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Marcotrigiano, J., (1997) Cell, 89, 951.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES1reservoir
210-12 %PEG40001reservoir
310 %isopropanol1reservoir
420 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 38968 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 7 % / Rsym value: 0.103
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 4 % / Rsym value: 0.259 / % possible all: 87.5
Reflection
*PLUS
Rmerge(I) obs: 0.103

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→20 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.252 3608 random
Rwork0.224 --
obs-35866 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 66 186 3246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24
LS refinement shellResolution: 1.8→1.81 Å /
RfactorNum. reflection
Rfree0.238 41
Rwork0.211 -
obs-370
Refinement
*PLUS
Rfactor obs: 0.224 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.238 / Rfactor Rwork: 0.211 / Rfactor obs: 0.211

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