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- PDB-5zk9: Stapled-peptides tailored against initiation of translation -

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Basic information

Entry
Database: PDB / ID: 5zk9
TitleStapled-peptides tailored against initiation of translation
Components
  • ACE-ARG-ILE-ILE-TYR-SER-ARG-MK8-GLN-LEU-LEU-MK8-LEU-LYS-NH2
  • Eukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN / Cap dependent Translation
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
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 / DI(HYDROXYETHYL)ETHER / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLama, D. / Liberator, A. / Frosi, Y. / Nakhle, J. / Tsomia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. ...Lama, D. / Liberator, A. / Frosi, Y. / Nakhle, J. / Tsomia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. / Ciesielski, F. / Uhring, M.
CitationJournal: Chem Sci / Year: 2019
Title: Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein.
Authors: Lama, D. / Liberatore, A.M. / Frosi, Y. / Nakhle, J. / Tsomaia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: ACE-ARG-ILE-ILE-TYR-SER-ARG-MK8-GLN-LEU-LEU-MK8-LEU-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8176
Polymers23,9742
Non-polymers8434
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-4 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.420, 38.080, 78.490
Angle α, β, γ (deg.)90.00, 122.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1254-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 22290.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: Protein/peptide ACE-ARG-ILE-ILE-TYR-SER-ARG-MK8-GLN-LEU-LEU-MK8-LEU-LYS-NH2


Mass: 1684.165 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The acetylation (ACE) and amidation (NH2) are included in the SEQRES.
Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 170 molecules

#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS BASED ON THE EIF4E INTERACTION ...AUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS BASED ON THE EIF4E INTERACTION SEQUENCE IN EIF4G (Q04637). IT SHOULD CORRESPOND TO THE FOLLOWING RESIDUES 608-620.

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% pEG1000 w/v, 12.5% PEG3350 w/v, 12.5% MPD w/v, 0.1M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.983994 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983994 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 22709 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rsym value: 0.048 / Net I/σ(I): 15.33
Reflection shellResolution: 1.76→1.86 Å / Mean I/σ(I) obs: 2.18 / Num. measured obs: 11964 / Num. unique obs: 3574 / Rsym value: 0.441

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPW

4tpw


Resolution: 1.76→45.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.399 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1136 5 %RANDOM
Rwork0.17709 ---
obs0.17881 21571 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.414 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20.11 Å2
2--0.07 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.76→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 54 166 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191762
X-RAY DIFFRACTIONr_bond_other_d0.0030.021636
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9872391
X-RAY DIFFRACTIONr_angle_other_deg1.35733785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80523.25686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07115308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.681515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021884
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02386
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_it1.3432.101794
X-RAY DIFFRACTIONr_mcbond_other1.3412.098792
X-RAY DIFFRACTIONr_mcangle_it2.1693.132990
X-RAY DIFFRACTIONr_mcangle_other2.173.131990
X-RAY DIFFRACTIONr_scbond_it1.9662.412968
X-RAY DIFFRACTIONr_scbond_other1.9642.412968
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0743.4981397
X-RAY DIFFRACTIONr_long_range_B_refined5.0724.9922056
X-RAY DIFFRACTIONr_long_range_B_other5.06925.0152057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.757→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 80 -
Rwork0.464 1512 -
obs--94.87 %

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