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- PDB-4ue8: Complex of D. melanogaster eIF4E with the 4E binding protein Thor -

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Basic information

Entry
Database: PDB / ID: 4ue8
TitleComplex of D. melanogaster eIF4E with the 4E binding protein Thor
Components
  • 4E-BINDING PROTEIN THOR
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


negative regulation of eukaryotic translation initiation factor 4F complex assembly / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / regulation of translation at presynapse, modulating synaptic transmission / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling ...negative regulation of eukaryotic translation initiation factor 4F complex assembly / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / regulation of translation at presynapse, modulating synaptic transmission / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / muscle cell postsynaptic specialization / RNA metabolic process / regulation of terminal button organization / neuronal ribonucleoprotein granule / regulation of mitochondrial translation / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / negative regulation of cell size / triglyceride metabolic process / response to starvation / vascular endothelial growth factor receptor signaling pathway / negative regulation of translational initiation / translation initiation factor activity / determination of adult lifespan / regulation of cell growth / translational initiation / response to bacterium / P-body / neuromuscular junction / cellular response to insulin stimulus / insulin receptor signaling pathway / antibacterial humoral response / presynapse / cellular response to oxidative stress / response to oxidative stress / nuclear body / immune response / translation / innate immune response / glutamatergic synapse / cytosol / cytoplasm
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
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Eukaryotic translation initiation factor 4E1 / Eukaryotic translation initiation factor 4E-binding protein
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2015
Title: Molecular Architecture of 4E-BP Translational Inhibitors Bound to Eif4E.
Authors: Peter, D. / Igreja, C. / Weber, R. / Wohlbold, L. / Weiler, C. / Ebertsch, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionDec 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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: 4E-BINDING PROTEIN THOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6625
Polymers25,4542
Non-polymers2083
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-29.4 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.450, 73.290, 38.260
Angle α, β, γ (deg.)90.00, 112.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 21249.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein/peptide 4E-BINDING PROTEIN THOR


Mass: 4204.940 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 50-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9XZ56
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE ...THE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE NUMBERS OF CHAIN A ARE SHIFTED BY -11 RESIDUES. NUMBERING CORRESPONDS TO UNP P48598-2 AND PDB 4AXG. THE FIRST FOUR RESIDUES OF CHAIN B REMAIN FROM THE EXPRESSION TAG.

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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: 2 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.2
Details: 0.2M KNO3, 0.5% N-OCTYL-BETA-D-GLUCOSIDE, 18% PEG3350, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→36.6 Å / Num. obs: 70124 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.03 / Net I/σ(I): 23.7
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4 / Rsym value: 0.32 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AXG CHAIN A

4axg


Resolution: 1.1→36.645 Å / SU ML: 0.07 / σ(F): 1.37 / Phase error: 15.15 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. NON-WATER ATOMS WERE REFINED WITH INDIVIDUAL ANISOTROPIC B-FACTORS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. NON-WATER ATOMS WERE REFINED WITH INDIVIDUAL ANISOTROPIC B-FACTORS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 73, 122, 156, 177, 193, 225. CHAIN B, RESIDUE 61. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 84 TO 90, 235 TO 248.
RfactorNum. reflection% reflection
Rfree0.1614 3555 5.1 %
Rwork0.1452 --
obs0.1461 70121 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.83 Å2
Refinement stepCycle: LAST / Resolution: 1.1→36.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 13 191 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071705
X-RAY DIFFRACTIONf_angle_d1.1682315
X-RAY DIFFRACTIONf_dihedral_angle_d12.715658
X-RAY DIFFRACTIONf_chiral_restr0.076251
X-RAY DIFFRACTIONf_plane_restr0.005294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.1150.18361250.17042409X-RAY DIFFRACTION86
1.115-1.1310.15421350.15382516X-RAY DIFFRACTION92
1.131-1.14790.16341240.1462569X-RAY DIFFRACTION92
1.1479-1.16580.15531470.13372546X-RAY DIFFRACTION93
1.1658-1.18490.16981390.1352595X-RAY DIFFRACTION93
1.1849-1.20530.14721400.13512586X-RAY DIFFRACTION94
1.2053-1.22730.14631350.13472608X-RAY DIFFRACTION94
1.2273-1.25090.16461480.12582609X-RAY DIFFRACTION95
1.2509-1.27640.16331280.12572650X-RAY DIFFRACTION94
1.2764-1.30420.16071240.12472536X-RAY DIFFRACTION93
1.3042-1.33450.14111310.12082618X-RAY DIFFRACTION94
1.3345-1.36790.15221360.11972662X-RAY DIFFRACTION95
1.3679-1.40480.16111410.12022657X-RAY DIFFRACTION97
1.4048-1.44620.15911330.11722678X-RAY DIFFRACTION96
1.4462-1.49290.15751320.12252714X-RAY DIFFRACTION98
1.4929-1.54620.14911710.11872725X-RAY DIFFRACTION98
1.5462-1.60810.14891540.11692736X-RAY DIFFRACTION99
1.6081-1.68130.13841270.1182800X-RAY DIFFRACTION100
1.6813-1.770.14321450.12812752X-RAY DIFFRACTION99
1.77-1.88090.16771470.13992751X-RAY DIFFRACTION100
1.8809-2.02610.14611570.13312763X-RAY DIFFRACTION100
2.0261-2.22990.1511530.14042788X-RAY DIFFRACTION99
2.2299-2.55250.17851800.15622723X-RAY DIFFRACTION99
2.5525-3.21560.17231570.1682763X-RAY DIFFRACTION100
3.2156-36.66530.16681460.16412812X-RAY DIFFRACTION99

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