[English] 日本語
Yorodumi
- PDB-6fc1: Crystal structure of the eIF4E-Eap1p complex from Saccharomyces c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fc1
TitleCrystal structure of the eIF4E-Eap1p complex from Saccharomyces cerevisiae in the cap-bound state
Components
  • Eukaryotic translation initiation factor 4E
  • Protein EAP1
KeywordsTRANSLATION / Gene expression Translation Translation initiation Translational control
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic initiation factor 4E binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic initiation factor 4E binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / cytoplasmic stress granule / regulation of cell cycle / negative regulation of translation / ribosome / mRNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
eIF4E-associated protein / eIF4E-associated protein / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E / Protein EAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGruener, S. / Valkov, E.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast.
Authors: Gruner, S. / Weber, R. / Peter, D. / Chung, M.Y. / Igreja, C. / Valkov, E. / Izaurralde, E.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
B: Protein EAP1
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,45512
Polymers58,8264
Non-polymers1,6298
Water9,260514
1
A: Eukaryotic translation initiation factor 4E
B: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1365
Polymers29,4132
Non-polymers7223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-33 kcal/mol
Surface area12680 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3207
Polymers29,4132
Non-polymers9075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-33 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.712, 121.726, 62.348
Angle α, β, γ (deg.)90.00, 132.02, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 21822.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CDC33, TIF45, YOL139C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07260
#2: Protein Protein EAP1 / eIF4E-associated protein 1


Mass: 7590.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: EAP1, YKL204W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36041
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MIB (sodium malonate:imidazole:boric acid in molar ratios of 2:3:3) buffer (pH 7.0) 21% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.35→46.32 Å / Num. obs: 108809 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rsym value: 0.045 / Net I/σ(I): 16.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.6 % / Num. measured obs: 33379 / Num. unique obs: 5058 / CC1/2: 0.643 / Rsym value: 1.284 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBZ, chain A

6fbz


Resolution: 1.35→46.317 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1683 5391 4.96 %
Rwork0.1377 --
obs0.1392 108796 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→46.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 102 514 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124196
X-RAY DIFFRACTIONf_angle_d1.2795727
X-RAY DIFFRACTIONf_dihedral_angle_d17.4721583
X-RAY DIFFRACTIONf_chiral_restr0.114607
X-RAY DIFFRACTIONf_plane_restr0.009744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36540.3611840.31863243X-RAY DIFFRACTION92
1.3654-1.38140.33031600.29873288X-RAY DIFFRACTION94
1.3814-1.39830.3771680.27773262X-RAY DIFFRACTION94
1.3983-1.4160.27221760.24693352X-RAY DIFFRACTION94
1.416-1.43460.27641860.22043314X-RAY DIFFRACTION95
1.4346-1.45430.24941620.20583384X-RAY DIFFRACTION96
1.4543-1.4750.24451900.17773360X-RAY DIFFRACTION97
1.475-1.49710.18941760.1563392X-RAY DIFFRACTION97
1.4971-1.52050.20071680.13633435X-RAY DIFFRACTION97
1.5205-1.54540.17891630.13373346X-RAY DIFFRACTION96
1.5454-1.5720.1711540.13163451X-RAY DIFFRACTION98
1.572-1.60060.19061750.13193472X-RAY DIFFRACTION98
1.6006-1.63140.17141810.12613451X-RAY DIFFRACTION98
1.6314-1.66470.16741660.12783498X-RAY DIFFRACTION99
1.6647-1.70090.18731810.12893479X-RAY DIFFRACTION99
1.7009-1.74050.17441870.12763480X-RAY DIFFRACTION99
1.7405-1.7840.16422040.1193468X-RAY DIFFRACTION99
1.784-1.83220.16491770.11733512X-RAY DIFFRACTION100
1.8322-1.88620.16192090.11573462X-RAY DIFFRACTION100
1.8862-1.9470.15171780.11773527X-RAY DIFFRACTION100
1.947-2.01660.16161910.12143496X-RAY DIFFRACTION100
2.0166-2.09740.14212030.11613476X-RAY DIFFRACTION100
2.0974-2.19280.1461940.11673506X-RAY DIFFRACTION100
2.1928-2.30840.14841710.12023543X-RAY DIFFRACTION100
2.3084-2.4530.18231770.12883517X-RAY DIFFRACTION100
2.453-2.64240.14692010.13143509X-RAY DIFFRACTION100
2.6424-2.90830.15941720.13243523X-RAY DIFFRACTION100
2.9083-3.32910.15491800.1343546X-RAY DIFFRACTION100
3.3291-4.19380.14791690.1273542X-RAY DIFFRACTION100
4.1938-46.34420.18231880.16583571X-RAY DIFFRACTION100

+
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