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- PDB-1ipb: CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1ipb
TitleCRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
KeywordsRNA BINDING PROTEIN / Initiation factor / Protein biosynthesis
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
Chem-GTA / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsTomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. ...Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / Ishikawa, M. / Miura, K.
CitationJournal: BIOCHEM.J. / Year: 2002
Title: Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor ...Title: Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor 4E: biological importance of the C-terminal flexible region
Authors: Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / ...Authors: Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / Ishikawa, M. / Miura, K.
History
DepositionMay 8, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9182
Polymers25,1301
Non-polymers7871
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.26, 89.26, 38.51
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E


Mass: 25130.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEMEX / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES-KOH1reservoirpH7.5
227 %(w/v)PEG60001reservoir
30.2 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 20089 / % possible obs: 82.6 % / Rmerge(I) obs: 0.0836

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementResolution: 2→30 Å / σ(F): 2
RfactorNum. reflection
Rfree0.229 1657
Rwork0.196 -
all-20843
obs-17165
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 51 138 1761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_d1.281
X-RAY DIFFRACTIONc_dihedral_angle_d22.24
X-RAY DIFFRACTIONc_improper_angle_d0.685
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 16683 / Rfactor obs: 0.196 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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