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- PDB-4ued: Complex of human eIF4E with the 4E binding protein 4E-BP1 -

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Basic information

Entry
Database: PDB / ID: 4ued
TitleComplex of human eIF4E with the 4E binding protein 4E-BP1
Components
  • EUKARYOTIC TRANSLATION FACTOR 4E-BINDING PROTEIN 1
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN / TRANSLATIONAL REPRESSION
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 / eukaryotic initiation factor 4E binding / 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 ...eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / 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 / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of neuron differentiation / Translation initiation complex formation / TOR signaling / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to dexamethasone stimulus / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translation initiation factor binding / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / 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 / cytoplasm / cytosol
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
Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Atomic model / Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION FACTOR 4E-BINDING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)25,9912
Polymers25,9912
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-14.4 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.110, 66.580, 43.050
Angle α, β, γ (deg.)90.00, 118.30, 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: 21657.625 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P06730
#2: Protein/peptide EUKARYOTIC TRANSLATION FACTOR 4E-BINDING PROTEIN 1 / 4E-BP1 / EIF4E-BINDING PROTEIN 1 / PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY ...4E-BP1 / EIF4E-BINDING PROTEIN 1 / PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY INSULIN 1 / PHAS-I


Mass: 4333.087 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q13541
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. THE FIRST FOUR RESIDUES OF CHAIN ...THE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 8.5
Details: 0.03M EACH DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 0.1M BICINE/TRIZMA BASE PH 8.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.75→37.9 Å / Num. obs: 20595 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 24.27 Å2 / Rsym value: 0.04 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.31 / % possible all: 98.1

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Processing

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

4tpw


Resolution: 1.75→37.906 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 24.46 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN B, RESIDUES 73, 74. THE FOLLOWING RESIDUES WERE MODELED AS ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN B, RESIDUES 73, 74. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 64, 92, 172. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 205 TO 211.
RfactorNum. reflection% reflection
Rfree0.2368 1083 5.3 %
Rwork0.1924 --
obs0.1946 20588 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 119 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041806
X-RAY DIFFRACTIONf_angle_d0.782449
X-RAY DIFFRACTIONf_dihedral_angle_d11.629679
X-RAY DIFFRACTIONf_chiral_restr0.032262
X-RAY DIFFRACTIONf_plane_restr0.003312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.82970.27741510.21162446X-RAY DIFFRACTION98
1.8297-1.92620.22661280.20642422X-RAY DIFFRACTION98
1.9262-2.04690.26171520.19812442X-RAY DIFFRACTION98
2.0469-2.20490.25211470.19762395X-RAY DIFFRACTION96
2.2049-2.42670.2421170.19042466X-RAY DIFFRACTION98
2.4267-2.77780.25941700.1962394X-RAY DIFFRACTION97
2.7778-3.49930.2583900.20292459X-RAY DIFFRACTION96
3.4993-37.91520.20751280.18032481X-RAY DIFFRACTION97

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