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

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Basic information

Entry
Database: PDB / ID: 5zml
TitleStapled-peptides tailored against initiation of translation
Components
  • ACE-LYS-LYS-ARG-TYR-SER-ARG-MK8-GLN-LEU-LEU-MK8-PHE-ARG-ARG
  • 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 / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of neuron differentiation / Translation initiation complex formation / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to dexamethasone stimulus / 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 / cytoplasm / cytosol
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
NITRATE ION / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLama, D. / Liberator, A. / Frosi, Y. / Nakhle, J. / Tsomia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. / Yano, J.
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
DepositionApr 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,6316
Polymers24,3832
Non-polymers2484
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint7 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.290, 91.610, 136.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1152-

HOH

21A-1169-

HOH

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Components

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


Mass: 22288.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pEMB54 / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: Protein/peptide ACE-LYS-LYS-ARG-TYR-SER-ARG-MK8-GLN-LEU-LEU-MK8-PHE-ARG-ARG


Mass: 2094.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS CORRESPONDS APPROXIMATELY TO SEQUENCE ...AUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS CORRESPONDS APPROXIMATELY TO SEQUENCE 609-624 OF EIF4G1 (Q04637). The residuess B8 and B12 are (S)-2-(4-pentenyl) alanine and form a aliphatic hydrocarbon staple via a ring closing metathesis reaction.

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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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 40%(v/v) Ethylene glycol, 20 %(w/v) PEG 8000, 0.3M Sodium nitrate, 0.3M Ammonium sulfate, 100mM Sodium HEPES/MOPS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→68.42 Å / Num. obs: 22468 / % possible obs: 98.3 % / Redundancy: 6.1 % / Rsym value: 0.088 / Net I/σ(I): 13.05
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 3.17 / Num. measured obs: 8825 / Num. unique obs: 1588 / Rsym value: 0.451 / % possible all: 95.7

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Processing

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

4bea


Resolution: 1.8→68.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.822 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22259 2088 9.3 %RANDOM
Rwork0.18471 ---
obs0.18825 20343 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.189 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20 Å2
2---0.54 Å20 Å2
3----2.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→68.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 16 190 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191744
X-RAY DIFFRACTIONr_bond_other_d0.0020.021589
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9522357
X-RAY DIFFRACTIONr_angle_other_deg0.93833667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49723.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88215295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3551515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
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_it1.5852.525822
X-RAY DIFFRACTIONr_mcbond_other1.5742.523821
X-RAY DIFFRACTIONr_mcangle_it2.5483.7711024
X-RAY DIFFRACTIONr_mcangle_other2.5473.7731025
X-RAY DIFFRACTIONr_scbond_it1.7982.684922
X-RAY DIFFRACTIONr_scbond_other1.7962.684922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9063.9291333
X-RAY DIFFRACTIONr_long_range_B_refined4.66629.4062063
X-RAY DIFFRACTIONr_long_range_B_other4.66529.4092064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 141 -
Rwork0.242 1444 -
obs--95.6 %

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