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- PDB-5t46: Crystal structure of the human eIF4E-eIF4G complex -

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Basic information

Entry
Database: PDB / ID: 5t46
TitleCrystal structure of the human eIF4E-eIF4G complex
Components
  • Eukaryotic translation initiation factor 4 gamma 1
  • Eukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E-BINDING PROTEIN / TRANSLATION INITIATION / eIF4F
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / regulation of translation at postsynapse, modulating synaptic transmission ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / 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 / positive regulation of protein localization to cell periphery / RISC complex / regulation of translational initiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / cellular response to nutrient levels / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / translation initiation factor binding / energy homeostasis / translational initiation / positive regulation of neuron differentiation / positive regulation of protein metabolic process / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / negative regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / P-body / lung development / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / ISG15 antiviral mechanism / neuron differentiation / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / regulation of translation / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / postsynapse / response to ethanol / DNA-binding transcription factor binding / negative regulation of translation / molecular adaptor activity / ribosome / nuclear speck / translation / mRNA binding / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Initiation factor 4G / 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 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. ...Initiation factor 4G / 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 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / Translation Initiation factor eIF- 4e-like / W2 domain / W2 domain profile. / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGruener, S. / Peter, D. / Weber, R. / Wohlbold, L. / Chung, M.-Y. / Weichenrieder, O. / Valkov, E. / Igreja, C. / Izaurralde, E.
CitationJournal: Mol.Cell / Year: 2016
Title: The Structures of eIF4E-eIF4G Complexes Reveal an Extended Interface to Regulate Translation Initiation.
Authors: Gruner, S. / Peter, D. / Weber, R. / Wohlbold, L. / Chung, M.Y. / Weichenrieder, O. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Jan 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

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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: Eukaryotic translation initiation factor 4 gamma 1
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48113
Polymers66,7604
Non-polymers1,7219
Water6,233346
1
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1025
Polymers33,3802
Non-polymers7223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-19 kcal/mol
Surface area11120 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3788
Polymers33,3802
Non-polymers9996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-20 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.250, 70.347, 79.913
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E / EIF4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 25503.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: PETMCN / Details (production host): (PNYC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P06730
#2: Protein Eukaryotic translation initiation factor 4 gamma 1 / / eIF-4G1 / p220


Mass: 7876.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4G1, EIF4F, EIF4G, EIF4GI / Plasmid: PETMCN / Details (production host): (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q04637
#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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25 / Details: 0.1 M Hepes pH 7.25, 25% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.53→44.65 Å / Num. obs: 74453 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 25 Å2 / CC1/2: 0.998 / Rsym value: 0.052 / Net I/σ(I): 11.6
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.565 / Rsym value: 1.013 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPW

4tpw


Resolution: 1.53→44.647 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 16.69
Details: TORSIONAL NCS RESTRAINTS WERE APPLIED RELATING CHAINS A, B TO CHAINS C, D. INDIVIDUAL B-FACTORS WERE REFINED ANISOTROPICALLY EXCEPT FOR WATER ATOMS. HYDROGENS WERE REFINED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1619 3681 4.95 %
Rwork0.1389 70730 -
obs0.1401 74411 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 1.53→44.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 108 346 3975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083782
X-RAY DIFFRACTIONf_angle_d0.9185128
X-RAY DIFFRACTIONf_dihedral_angle_d13.5912270
X-RAY DIFFRACTIONf_chiral_restr0.053527
X-RAY DIFFRACTIONf_plane_restr0.006670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55020.29641430.25652716X-RAY DIFFRACTION100
1.5502-1.57140.2641440.23632716X-RAY DIFFRACTION100
1.5714-1.59380.24611290.21752684X-RAY DIFFRACTION100
1.5938-1.61760.2681300.21332755X-RAY DIFFRACTION100
1.6176-1.64290.21291370.20242712X-RAY DIFFRACTION100
1.6429-1.66990.23791510.18832710X-RAY DIFFRACTION100
1.6699-1.69860.23171470.18272704X-RAY DIFFRACTION100
1.6986-1.72950.22721680.17852645X-RAY DIFFRACTION100
1.7295-1.76280.21371330.17342733X-RAY DIFFRACTION100
1.7628-1.79880.20331450.15422711X-RAY DIFFRACTION100
1.7988-1.83790.17011450.13772675X-RAY DIFFRACTION100
1.8379-1.88070.16151490.12232746X-RAY DIFFRACTION100
1.8807-1.92770.17171370.11892675X-RAY DIFFRACTION100
1.9277-1.97980.15141720.11642714X-RAY DIFFRACTION100
1.9798-2.03810.13081310.112718X-RAY DIFFRACTION100
2.0381-2.10380.14941650.11472675X-RAY DIFFRACTION100
2.1038-2.1790.15181270.1212740X-RAY DIFFRACTION100
2.179-2.26630.15241170.11782774X-RAY DIFFRACTION100
2.2663-2.36940.1511360.11472715X-RAY DIFFRACTION100
2.3694-2.49430.15581440.12762720X-RAY DIFFRACTION100
2.4943-2.65060.16271420.12432733X-RAY DIFFRACTION100
2.6506-2.85520.16621470.13862707X-RAY DIFFRACTION100
2.8552-3.14250.15061250.13282749X-RAY DIFFRACTION100
3.1425-3.5970.15171340.13322744X-RAY DIFFRACTION100
3.597-4.53120.13481410.13242752X-RAY DIFFRACTION100
4.5312-44.66590.17081420.1662807X-RAY DIFFRACTION99

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