[English] 日本語
Yorodumi
- PDB-1ej4: COCRYSTAL STRUCTURE OF EIF4E/4E-BP1 PEPTIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ej4
TitleCOCRYSTAL STRUCTURE OF EIF4E/4E-BP1 PEPTIDE
Components
  • EUKARYOTIC INITIATION FACTOR 4E
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E BINDING PROTEIN 1
KeywordsTRANSLATION / eIF4E/4E-BP/7-methyl-GDP
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / 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 / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / stem cell population maintenance / negative regulation of neuron differentiation / TOR signaling / mTORC1-mediated signalling / cellular response to dexamethasone stimulus / behavioral fear response / mRNA export from nucleus / translation initiation factor binding / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / nuclear body / translation / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / 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'-DIPHOSPHATE / : / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsMarcotrigiano, J. / Gingras, A.-C. / Sonenberg, N. / Burley, S.K.
CitationJournal: Mol.Cell / Year: 1999
Title: Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G.
Authors: Marcotrigiano, J. / Gingras, A.C. / Sonenberg, N. / Burley, S.K.
History
DepositionFeb 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EUKARYOTIC INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4653
Polymers24,0062
Non-polymers4581
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.900, 45.200, 62.100
Angle α, β, γ (deg.)90.00, 101.8, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein EUKARYOTIC INITIATION FACTOR 4E


Mass: 22145.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3B / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 4E BINDING PROTEIN 1


Mass: 1861.240 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-67 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS)
References: GenBank: 4758258, UniProt: Q13541*PLUS
#3: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 %PEG40001reservoir
210 %isopropanol1reservoir
30.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 10817 / % possible obs: 97.4 % / Observed criterion σ(I): 5 / Redundancy: 4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.103 / % possible all: 84.8
Reflection shell
*PLUS
% possible obs: 84.8 %

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→25 Å / σ(F): 2
RfactorSelection details
Rfree0.267 10% of the data
Rwork0.219 -
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 29 85 1713
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.55

+
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