- PDB-4dum: Co-crystal structure of eIF4E with inhibitor -
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Basic information
Entry
Database: PDB / ID: 4dum
Title
Co-crystal structure of eIF4E with inhibitor
Components
Eukaryotic translation initiation factor 4E
Keywords
TRANSLATION / 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Deadenylation of mRNA / mRNA cap binding / Transport of the SLBP independent Mature 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Deadenylation of mRNA / mRNA cap binding / Transport of the SLBP independent Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / stem cell population maintenance / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / 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 / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / 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 / cytoplasm / cytosol Similarity search - Function
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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal grow
Temperature: 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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 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 shell
Resolution: 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
Name
Version
Classification
StructureStudio
datacollection
MOLREP
phasing
REFMAC
5.5.0109
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2711
292
4.7 %
RANDOM
Rwork
0.20176
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obs
0.20497
5969
98.46 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 35.343 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.08 Å2
0 Å2
0 Å2
2-
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1.51 Å2
0 Å2
3-
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-1.43 Å2
Refinement step
Cycle: LAST / Resolution: 2.95→38.236 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1547
0
40
14
1601
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1641
X-RAY DIFFRACTION
r_angle_refined_deg
1.506
1.953
2222
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.718
5
189
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.487
23.929
84
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.904
15
284
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.663
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
228
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1255
X-RAY DIFFRACTION
r_mcbond_it
0.818
1.5
935
X-RAY DIFFRACTION
r_mcangle_it
1.581
2
1512
X-RAY DIFFRACTION
r_scbond_it
1.835
3
706
X-RAY DIFFRACTION
r_scangle_it
3.215
4.5
708
LS refinement shell
Resolution: 2.95→3.027 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.401
19
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Rwork
0.276
401
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obs
-
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97.22 %
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