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- PDB-6fbz: Crystal structure of the eIF4E-eIF4G complex from Chaetomium ther... -

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Basic information

Entry
Database: PDB / ID: 6fbz
TitleCrystal structure of the eIF4E-eIF4G complex from Chaetomium thermophilum in the cap-bound state
Components
  • Eukaryotic translation initiation factor 4E-like protein,Eukaryotic translation initiation factor 4E-like protein
  • Eukaryotic translation initiation factor 4G
KeywordsTRANSLATION / Translation Translational control Translation initiation Gene expression
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / mRNA binding
Similarity search - Function
Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / 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 ...Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / 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 / 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-like protein / MIF4G domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E-like protein,Eukaryotic translation initiation factor 4E-like protein
B: Eukaryotic translation initiation factor 4G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6683
Polymers32,1302
Non-polymers5381
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-36 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.960, 75.354, 48.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Eukaryotic translation initiation factor 4E-like protein,Eukaryotic translation initiation factor 4E-like protein


Mass: 23081.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0058450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SCU4
#2: Protein Eukaryotic translation initiation factor 4G


Mass: 9048.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0071550 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SFP0
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.82 Å3/Da / Density % sol: 32.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20000 20% PEG 500 MME 0.02 M 1,6-hexanediol 0.02 M 1-butanol 0.02 M (RS)-1,2-propanediol 0.02 M 2-propanol 0.02 M 1,4-butanediol 0.02 M 1,3-propanediol 0.1 M Bicine/Trizma pH 8.5 0.687 mM m7GpppG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→75.35 Å / Num. obs: 38441 / % possible obs: 99.6 % / Redundancy: 12.7 % / Rsym value: 0.074 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1742 / CC1/2: 0.416 / Rsym value: 1.913 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPW

4tpw


Resolution: 1.496→48.763 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.2058 1941 5.06 %
Rwork0.1699 --
obs0.1718 38394 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.496→48.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 33 134 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222311
X-RAY DIFFRACTIONf_angle_d1.6693145
X-RAY DIFFRACTIONf_dihedral_angle_d19.05876
X-RAY DIFFRACTIONf_chiral_restr0.114331
X-RAY DIFFRACTIONf_plane_restr0.012419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4963-1.53370.29461450.26152441X-RAY DIFFRACTION95
1.5337-1.57520.28761260.2432618X-RAY DIFFRACTION100
1.5752-1.62150.26461360.22232537X-RAY DIFFRACTION100
1.6215-1.67390.27481410.21542599X-RAY DIFFRACTION100
1.6739-1.73370.23911180.20282581X-RAY DIFFRACTION100
1.7337-1.80310.23741210.18812599X-RAY DIFFRACTION100
1.8031-1.88520.22621350.16822593X-RAY DIFFRACTION100
1.8852-1.98460.20781470.15692579X-RAY DIFFRACTION100
1.9846-2.10890.21941540.16242596X-RAY DIFFRACTION100
2.1089-2.27170.18351390.15632583X-RAY DIFFRACTION100
2.2717-2.50030.19981280.15842643X-RAY DIFFRACTION100
2.5003-2.86210.21781410.1682637X-RAY DIFFRACTION100
2.8621-3.60580.19351390.1632664X-RAY DIFFRACTION100
3.6058-48.78850.19121710.16732783X-RAY DIFFRACTION100

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