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- PDB-5zk5: Stapled-peptides tailored against initiation of translation -

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Basic information

Entry
Database: PDB / ID: 5zk5
TitleStapled-peptides tailored against initiation of translation
Components
  • Eukaryotic translation initiation factor 4E
  • LYS-ARG-TYR-SER-ARG-GLU-GLN-LEU-LEU-MK8-PHE-GLN-ARG-MK8
KeywordsRNA BINDING PROTEIN / Cap dependent Translation
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / : / positive regulation of translation in response to endoplasmic reticulum stress / eukaryotic initiation factor 4G binding / cap-dependent translational initiation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / regulation of cellular response to stress / RNA cap binding ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / : / positive regulation of translation in response to endoplasmic reticulum stress / eukaryotic initiation factor 4G binding / cap-dependent translational initiation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / regulation of cellular response to stress / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / mRNA cap binding / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / 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 / regulation of translational initiation / positive regulation of protein localization to cell periphery / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of neuron differentiation / Translation initiation complex formation / positive regulation of protein metabolic process / mTORC1-mediated signalling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / regulation of presynapse assembly / cellular response to dexamethasone stimulus / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / mRNA export from nucleus / cellular response to nutrient levels / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / translation initiation factor binding / translation initiation factor activity / positive regulation of neuron differentiation / positive regulation of mitotic cell cycle / negative regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / translational initiation / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / positive regulation of cell growth / molecular adaptor activity / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / ribosome / translation / mRNA binding / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / membrane / 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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain ...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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / refine_hist / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_low / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_asym_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 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: LYS-ARG-TYR-SER-ARG-GLU-GLN-LEU-LEU-MK8-PHE-GLN-ARG-MK8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8653
Polymers24,3262
Non-polymers5391
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.480, 65.090, 76.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
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-ARG-TYR-SER-ARG-GLU-GLN-LEU-LEU-MK8-PHE-GLN-ARG-MK8


Mass: 2035.482 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Stapled Peptide, N-Terminal Acetylation and C-Terminal Amidation
Source: (synth.) Homo sapiens (human) / References: UniProt: Q04637
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 609-623 of eIF4E (Q04637). The actual sequence is: Ac-KKRYSREQLL(S5)FQR(S5)-NH2 S5 corresponds to (S)-2-(4-pentenyl) alanine. This are linked together via RCM(ring closing metathesis) to form a hydrocarbon staples.

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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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30%(w/v) PEG6000, 0.1M Na-Hepes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.983998 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: 0.983998 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 9319 / % possible obs: 99.4 % / Redundancy: 8.7 % / Rsym value: 0.079 / Net I/σ(I): 16.11
Reflection shellResolution: 1.59→1.68 Å / Mean I/σ(I) obs: 3.13 / Num. measured obs: 8249 / Num. unique obs: 1457 / Rsym value: 0.464

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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: 2.25→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.962 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26839 465 5 %RANDOM
Rwork0.19826 ---
obs0.20176 8827 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.924 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å2-0 Å2
2---2.81 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 42 55 1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191708
X-RAY DIFFRACTIONr_bond_other_d0.0020.021539
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.9682321
X-RAY DIFFRACTIONr_angle_other_deg1.29533548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6223.29588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72515286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5411515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
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_it1.9413.594782
X-RAY DIFFRACTIONr_mcbond_other1.9363.585776
X-RAY DIFFRACTIONr_mcangle_it3.1055.374973
X-RAY DIFFRACTIONr_mcangle_other3.1025.364968
X-RAY DIFFRACTIONr_scbond_it2.2643.874926
X-RAY DIFFRACTIONr_scbond_other2.2633.875927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6145.7021349
X-RAY DIFFRACTIONr_long_range_B_refined5.2239.7181927
X-RAY DIFFRACTIONr_long_range_B_other5.21739.681919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 33 -
Rwork0.278 623 -
obs--97.91 %

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