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

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Basic information

Entry
Database: PDB / ID: 5zjy
TitleStapled-peptides tailored against initiation of translation
Components
  • Eukaryotic translation initiation factor 4E
  • LYS-LYS-ARG-TYR-SER-ARG-2JN-GLN-LEU-LEU-2JN-PHE
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 / Translation initiation complex formation / mTORC1-mediated signalling / negative regulation of neuron differentiation / 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 / cellular response to dexamethasone stimulus / translational initiation / P-body / neuron differentiation / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / 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 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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, B. / 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 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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: LYS-LYS-ARG-TYR-SER-ARG-2JN-GLN-LEU-LEU-2JN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4503
Polymers23,9112
Non-polymers5381
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-7 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.800, 39.800, 110.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 22290.334 Da / Num. of mol.: 1 / Fragment: UNP residues 28-217
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 LYS-LYS-ARG-TYR-SER-ARG-2JN-GLN-LEU-LEU-2JN-PHE


Mass: 1621.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-Terminal Acetylation, C-Terminal Amidation / Source: (synth.) Homo sapiens (human)
#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


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the chain B is a hybrid sequence which corresponds approximately to sequence 609- ...Authors state that the chain B is a hybrid sequence which corresponds approximately to sequence 609-624 of eIF4E (Q04637).

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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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30%(W/V) PEG 6000, 0.1M Na-Hepes pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97995 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 26096 / % possible obs: 94.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.56
Reflection shellResolution: 1.59→1.68 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.08 / Num. measured obs: 17265 / Num. unique obs: 4018 / % possible all: 99.1

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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: 1.59→34.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.931 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21605 1305 5 %RANDOM
Rwork0.17826 ---
obs0.18011 24791 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.59→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 33 149 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191687
X-RAY DIFFRACTIONr_bond_other_d0.0020.021526
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9762301
X-RAY DIFFRACTIONr_angle_other_deg0.92633520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24623.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2731514
X-RAY DIFFRACTIONr_chiral_restr0.3390.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
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_it1.8632.718778
X-RAY DIFFRACTIONr_mcbond_other1.852.712776
X-RAY DIFFRACTIONr_mcangle_it3.0314.059970
X-RAY DIFFRACTIONr_mcangle_other3.0364.058970
X-RAY DIFFRACTIONr_scbond_it2.2372.985909
X-RAY DIFFRACTIONr_scbond_other2.2362.987910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.554.3821327
X-RAY DIFFRACTIONr_long_range_B_refined5.36331.5651986
X-RAY DIFFRACTIONr_long_range_B_other5.26631.1261956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.588→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 84 -
Rwork0.324 1603 -
obs--88.09 %

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