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- PDB-3am7: Crystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide -

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Basic information

Entry
Database: PDB / ID: 3am7
TitleCrystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide
Components
  • Eukaryotic translation initiation factor 4E-binding protein 2
  • Eukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION/PROTEIN BINDING / Cap / TRANSLATION / PROTEIN-PROTEIN COMPLEX / TRANSLATION-PROTEIN BINDING complex
Function / homology
Function and homology information


neuronal ribonucleoprotein granule / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E 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 ...neuronal ribonucleoprotein granule / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E 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 / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / 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 / intracellular non-membrane-bounded organelle / stem cell population maintenance / TOR signaling / mTORC1-mediated signalling / social behavior / 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 / negative regulation of translational initiation / translation repressor activity / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / regulation of synaptic plasticity / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / cytoplasmic ribonucleoprotein granule / ISG15 antiviral mechanism / memory / neuron differentiation / cytoplasmic stress granule / regulation of translation / insulin receptor signaling pathway / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTomoo, K. / Fukuyo, A. / In, Y. / Ishida, T.
CitationJournal: J.Pept.Sci. / Year: 2011
Title: Structural scaffold for eIF4E binding selectivity of 4E-BP isoforms: crystal structure of eIF4E binding region of 4E-BP2 and its comparison with that of 4E-BP1.
Authors: Fukuyo, A. / In, Y. / Ishida, T. / Tomoo, K.
History
DepositionAug 17, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _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

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1093
Polymers24,5712
Non-polymers5381
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-4 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.84, 87.84, 37.75
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 / eIF-4E / eIF4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22288.252 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 2 / eIF4E-binding protein 2 / 4E-BP2


Mass: 2282.627 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 47-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4EBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13542
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG-MME 2000, 0.1M MES, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→43.9 Å / Num. obs: 16434 / % possible obs: 95.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.81 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8
Reflection shellResolution: 2.1→43.9 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 8 / Num. unique all: 16434 / % possible all: 95.4

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.3 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.268 734 -
Rwork0.23 --
obs-14502 97.1 %
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 33 93 1851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.685
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.31

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