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- PDB-4dum: Co-crystal structure of eIF4E with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4dum
TitleCo-crystal structure of eIF4E with inhibitor
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / CAP-binding protein / translation initiation factor / m7GTP
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / 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 / mRNA cap binding / Deadenylation of mRNA ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / 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 / mRNA cap binding / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / 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 / Translation initiation complex formation / stem cell population maintenance / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Chem-HLI / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMin, X. / Johnstone, S. / Walker, N. / Wang, Z.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structure-Guided Design, Synthesis, and Evaluation of Guanine-Derived Inhibitors of the eIF4E mRNA-Cap Interaction.
Authors: Chen, X. / Kopecky, D.J. / Mihalic, J. / Jeffries, S. / Min, X. / Heath, J. / Deignan, J. / Lai, S. / Fu, Z. / Guimaraes, C. / Shen, S. / Li, S. / Johnstone, S. / Thibault, S. / Xu, H. / ...Authors: Chen, X. / Kopecky, D.J. / Mihalic, J. / Jeffries, S. / Min, X. / Heath, J. / Deignan, J. / Lai, S. / Fu, Z. / Guimaraes, C. / Shen, S. / Li, S. / Johnstone, S. / Thibault, S. / Xu, H. / Cardozo, M. / Shen, W. / Walker, N. / Kayser, F. / Wang, Z.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6404
Polymers28,0401
Non-polymers6003
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.225, 58.766, 125.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28040.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: Chemical ChemComp-HLI / (4-{7-[2-(4-chlorophenoxy)ethyl]-2-(methylamino)-6-oxo-6,7-dihydro-1H-purin-8-yl}phenyl)phosphonic acid


Mass: 475.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN5O5P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: The purified protein which contained 100 uM m7-GTP was then concentrated to about 7 mg/mL in 20 mM Hepes, pH7.6, 100 mM KCl, 1mM DTT, 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e ...Details: The purified protein which contained 100 uM m7-GTP was then concentrated to about 7 mg/mL in 20 mM Hepes, pH7.6, 100 mM KCl, 1mM DTT, 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 1, 2007 / Details: Rigaku Varimax HR optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.95→62.75 Å / Num. all: 18074 / Num. obs: 6282 / % possible obs: 98.9 % / Observed criterion σ(I): 2.9 / Redundancy: 2.9 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.3 / Num. unique all: 765 / % possible all: 97.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→38.236 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.852 / SU B: 16.91 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 292 4.7 %RANDOM
Rwork0.20176 ---
obs0.20497 5969 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--1.51 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 40 14 1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221641
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9532222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48723.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6631512
X-RAY DIFFRACTIONr_chiral_restr0.10.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211255
X-RAY DIFFRACTIONr_mcbond_it0.8181.5935
X-RAY DIFFRACTIONr_mcangle_it1.58121512
X-RAY DIFFRACTIONr_scbond_it1.8353706
X-RAY DIFFRACTIONr_scangle_it3.2154.5708
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 19 -
Rwork0.276 401 -
obs--97.22 %

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