[English] 日本語
Yorodumi
- PDB-5zjz: Stapled-peptides tailored against initiation of translation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zjz
TitleStapled-peptides tailored against initiation of translation
Components
  • Eukaryotic translation initiation factor 4 gamma 1
  • 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
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 22, 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6373
Polymers24,0982
Non-polymers5391
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-9 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.270, 38.300, 78.930
Angle α, β, γ (deg.)90.00, 122.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

-
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 Eukaryotic translation initiation factor 4 gamma 1 / eIF-4G1


Mass: 1807.255 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Stapled Peptide, N-Terminal Acetylation and C-Terminal Amidation
Source: (synth.) Homo sapiens (human)
#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.: 100 / 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5%(w/v) PEG20000, 20%(w/v) PEG MME 550, 0.1M MES/imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 26192 / % possible obs: 97.6 % / Redundancy: 5.7 % / Rsym value: 0.057 / Net I/σ(I): 14.28
Reflection shellResolution: 1.67→1.78 Å / Mean I/σ(I) obs: 2.26 / Rsym value: 0.628 / % possible all: 94.4

-
Processing

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

4tpw


Resolution: 1.67→45.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.14 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1310 5 %RANDOM
Rwork0.18952 ---
obs0.19068 24882 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.02 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.67→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 33 100 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0020.021577
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9722367
X-RAY DIFFRACTIONr_angle_other_deg0.91633644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97223.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2441515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
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_it1.0951.904788
X-RAY DIFFRACTIONr_mcbond_other1.0931.903786
X-RAY DIFFRACTIONr_mcangle_it1.8892.838982
X-RAY DIFFRACTIONr_mcangle_other1.8912.838982
X-RAY DIFFRACTIONr_scbond_it1.3622.096950
X-RAY DIFFRACTIONr_scbond_other1.3612.096951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2343.0741382
X-RAY DIFFRACTIONr_long_range_B_refined4.0221.4771978
X-RAY DIFFRACTIONr_long_range_B_other3.67521.0371947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.674→1.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 89 -
Rwork0.382 1686 -
obs--89.83 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more