[English] 日本語
Yorodumi
- PDB-5gw6: Water-Bridge Mediates Recognition of mRNA Cap in eIF4E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gw6
TitleWater-Bridge Mediates Recognition of mRNA Cap in eIF4E
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Cap-dependent / Cap-free
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 / Transport of the SLBP independent Mature mRNA ...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 / 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 / stem cell population maintenance / Ribosomal scanning and start codon recognition / 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 / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / translational initiation / P-body / ISG15 antiviral mechanism / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / neuron differentiation / 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
Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBrown, C.J.
CitationJournal: Structure / Year: 2017
Title: Water-Bridge Mediates Recognition of mRNA Cap in eIF4E
Authors: Lama, D. / Pradhan, M.R. / Brown, C.J. / Eapen, R.S. / Joseph, T.L. / Kwoh, C.K. / Lane, D.P. / Verma, C.S.
History
DepositionSep 8, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 19, 2016ID: 5ABI
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,9804
Polymers22,7041
Non-polymers2763
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.695, 128.024, 38.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-501-

HOH

-
Components

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


Mass: 22703.631 Da / Num. of mol.: 1 / Mutation: E105A, K106A, K108A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06730
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3 Å3/Da / Density % sol: 58.98 % / Description: Long needle
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 5000 MME, 100MM TRIS BIS PH 5.0, 0.05M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2015
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→20 Å / Num. obs: 21660 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W97

2w97


Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.374 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22758 1105 5.1 %RANDOM
Rwork0.19673 ---
obs0.19833 20519 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å2-0 Å2
2---0.47 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 18 101 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191550
X-RAY DIFFRACTIONr_bond_other_d0.0030.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9312095
X-RAY DIFFRACTIONr_angle_other_deg0.98533330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14523.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52615262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3041512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it1.8261.803726
X-RAY DIFFRACTIONr_mcbond_other1.8261.802725
X-RAY DIFFRACTIONr_mcangle_it2.952.687904
X-RAY DIFFRACTIONr_mcangle_other2.9492.687905
X-RAY DIFFRACTIONr_scbond_it2.6042.188822
X-RAY DIFFRACTIONr_scbond_other2.5972.188822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1423.1471191
X-RAY DIFFRACTIONr_long_range_B_refined6.46615.6991846
X-RAY DIFFRACTIONr_long_range_B_other6.46315.6991846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 69 -
Rwork0.191 1489 -
obs--97.31 %

+
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