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- PDB-7ezw: Cyclic Peptide that Interacts with the eIF4E Capped-mRNA Binding Site -

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Basic information

Entry
Database: PDB / ID: 7ezw
TitleCyclic Peptide that Interacts with the eIF4E Capped-mRNA Binding Site
Components
  • ALA-CYS-GLU-MET-GLY-PHE-PHE-GLN-ASP-CYS-GLY
  • Eukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN/INHIBITOR / ap dependent translation / RNA BINDING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding ...eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / 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 / stem cell population maintenance / negative regulation of neuron differentiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mTORC1-mediated signalling / cellular response to dexamethasone stimulus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBrown, C.J. / Ng, S. / Frosi, Y.
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Development of a novel peptide aptamer that interacts with the eIF4E capped-mRNA binding site using peptide epitope linker evolution (PELE).
Authors: Frosi, Y. / Ng, S. / Lin, Y.C. / Jiang, S. / Ramlan, S.R. / Lama, D. / Verma, C.S. / Asial, I. / Brown, C.J.
History
DepositionJun 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _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.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Item: _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: ALA-CYS-GLU-MET-GLY-PHE-PHE-GLN-ASP-CYS-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3593
Polymers26,3362
Non-polymers231
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Protein interacts with peptide ligand via 1:1 binding model.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-11 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.139, 81.139, 66.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-301-

NA

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Components

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


Mass: 25130.242 Da / Num. of mol.: 1
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 ALA-CYS-GLU-MET-GLY-PHE-PHE-GLN-ASP-CYS-GLY


Mass: 1205.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: amidation / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium chloride 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→48.194 Å / Num. obs: 10511 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BEA

4bea


Resolution: 2.35→48.19 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.698 / SU ML: 0.178 / Cross valid method: FREE R-VALUE / ESU R: 0.332 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.248 579 5.554 %
Rwork0.205 --
obs-10425 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.245 Å20.123 Å20 Å2
2--0.245 Å20 Å2
3----0.796 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 1 59 1591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131569
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181458
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.6382120
X-RAY DIFFRACTIONr_angle_other_deg1.0891.5963345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26422.02194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3861512
X-RAY DIFFRACTIONr_chiral_restr0.0390.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined0.1680.2258
X-RAY DIFFRACTIONr_nbd_other0.1240.227
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2728
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.274
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_it1.2213.475742
X-RAY DIFFRACTIONr_mcbond_other1.2223.472739
X-RAY DIFFRACTIONr_mcangle_it2.1765.201923
X-RAY DIFFRACTIONr_mcangle_other2.1775.199921
X-RAY DIFFRACTIONr_scbond_it1.1783.601827
X-RAY DIFFRACTIONr_scbond_other1.1773.602828
X-RAY DIFFRACTIONr_scangle_it2.0685.3281197
X-RAY DIFFRACTIONr_scangle_other2.0675.3291198
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å
RfactorNum. reflection% reflection
Rfree0.296 51 -
Rwork0.264 708 -
obs--100 %

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