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- PDB-4aza: Improved eIF4E binding peptides by phage display guided design. -

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Basic information

Entry
Database: PDB / ID: 4aza
TitleImproved eIF4E binding peptides by phage display guided design.
Components
  • EIF4G1_D5S PEPTIDE
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
KeywordsTRANSLATION
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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / cap-dependent translational initiation / 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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / cap-dependent translational initiation / 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 / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / 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 / stem cell population maintenance / negative regulation of neuron differentiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of protein metabolic process / mTORC1-mediated signalling / cellular response to dexamethasone stimulus / positive regulation of G1/S transition of mitotic cell cycle / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA export from nucleus / cellular response to nutrient levels / behavioral fear response / energy homeostasis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / P-body / translational initiation / 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 / DNA-binding transcription factor binding / molecular adaptor activity / 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 / 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 / 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
Chem-MGO / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsChew, W.Z. / Quah, S.T. / Verma, C.S. / Liu, Y. / Lane, D.P. / Brown, C.J.
CitationJournal: Plos One / Year: 2012
Title: Improved Eif4E Binding Peptides by Phage Display Guided Design: Plasticity of Interacting Surfaces Yield Collective Effects.
Authors: Zhou, W. / Quah, S.T. / Verma, C.S. / Liu, Y. / Lane, D.P. / Brown, C.J.
History
DepositionJun 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: EIF4G1_D5S PEPTIDE
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: EIF4G1_D5S PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4796
Polymers53,4044
Non-polymers1,0742
Water3,927218
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EIF4G1_D5S PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2393
Polymers26,7022
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-7.9 kcal/mol
Surface area11120 Å2
MethodPISA
2
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: EIF4G1_D5S PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2393
Polymers26,7022
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-7.2 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.662, 38.168, 121.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF-4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 25130.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06730
#2: Protein/peptide EIF4G1_D5S PEPTIDE


Mass: 1571.888 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-TERMINAL IS ACETYLATED AND C-TERMINAL IS AMIDATED.
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q04637*PLUS
#3: Chemical ChemComp-MGO / [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE


Mass: 537.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.42 % / Description: NONE
Crystal growpH: 5 / Details: 20% PEG 5000 MME, 100 MM BISTRIS PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PROTEUM / Wavelength: 1.5418
DetectorType: RIGAKU PT 135 / Detector: CCD / Date: Apr 1, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→60.88 Å / Num. obs: 30410 / % possible obs: 99.3 % / Observed criterion σ(I): 8 / Redundancy: 9.22 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.22
Reflection shellResolution: 2.16→2.26 Å / Redundancy: 6.51 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.38 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W97

2w97


Resolution: 2.16→121.76 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.849 / SU B: 6.491 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27859 1532 5 %RANDOM
Rwork0.23292 ---
obs0.23526 30410 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.461 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å2-0.19 Å2
2---0.75 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.16→121.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 66 218 3604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023472
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9654701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1823.409176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6871528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212614
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
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: 2.158→2.214 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 86 -
Rwork0.296 1873 -
obs--90.74 %

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