semet substituted crystal  (Brookhaven Instruments)

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Three-dimensional structure of T. cruzi EIF4E5. ( A ) Overall superposition of TcEIF4E5 in complex with m 7 GTP, cap-1 and cap-4 (light pink, magenta and purple, respectively). (B–D) Electron density maps corresponding to the cap analogues. The ligands m 7 GTP ( B ), cap-1 ( C ) and cap-4 ( D ) are clearly defined by the electron density, except for the base moiety of cap-1 second nucleotide. 2 F o – F c electron density maps are represented in gray and contoured at 1.0σ. The ligands are represented in sticks. The region connecting β1–β2 strands (S1–S2) is indicated.

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques:

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: T. cruzi EIF4E5 cap recognition site. ( A ) Representation of the cap-4 binding site. Residues involved in the interaction with cap-4 are shown in sticks and labeled. The regions connecting β1–β2, β3–β4 and β5–β6 strands (S1–S2, S3–S4 and S5–S6) are indicated. ( B ) Three-dimensional structure of cap-4 evidencing the AACU base stacking. ( C ) Schematic representation showing the cap-4-TcEIF4E5 interactions in detail. Hydrophobic interactions are represented in dashed red and hydrogen bonds in blue dotted lines. The atoms involved in the hydrogen bonds are indicated in parentheses. Water molecules are represented as blue spheres.

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Binding Assay, Labeling

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Structural comparison of T. cruzi EIF4E5 with other eukaryotic IF4E factors. ( A ) Overall superposition: TcEIF4E5 is shown in purple, human eIF4E1 and eIF4E2 (HsIF4E1, PDB 1IPC; HsIF4E2, PDB 2JGB) are represented in green and orange, respectively. Mouse eIF4E3 (MmIF4E3, PDB: 4B6U) is represented in cyan. TcEIF4E5-bound cap-4 and HsIF4E1-bound m 7 GTP are shown in sticks. The regions connecting β1–β2, β3–β4 and β5–β6 strands (S1–S2, S3–S4 and S5–S6) are indicated. (B, C and D) Detailed comparison between the m 7 GTP recognition sites. ( B ) TcEIF4E5-cap-4 (purple) versus HsIF4E1-m7GTP (green), ( C ) TcEIF4E5-cap-4 (purple) versus HsIF4E2-m7GTP (orange), ( D ) TcEIF4E5-cap-4 (purple) versus MmIF4E3-m7GTP (cyan). Cap-4 is represented in purple and m 7 GTP follows the color of the counterpart structure. The m 7 G group position is indicated. Residues involved in the interaction with cap analogues are shown in sticks and labeled, following the color of the protein structure.

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Labeling

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Structural comparison of T. cruzi EIF4E5-cap-4 complex and L. major EIF4E1 in the apo state. ( A ) Overall superposition: TcEIF4E5 is shown in purple and LmEIF4E1 (PDB 5WB5) is shown in gray. ( B ) Detailed comparison of the cap recognition sites. Cap-4 is represented in yellow. TcEIF4E5 residues involved in the interaction with cap-4 and corresponding residues in LmEIF4E1 are shown in sticks and labeled, following the color of the protein structure. The regions connecting β1-β2, β3-β4 and β5-β6 strands (S1–S2, S3–S4 and S5–S6) are indicated.

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Labeling

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Electrostatic potential surface of ( A ) T. cruzi EIF4E5 and ( B ) L. major EIF4E1 (PDB 5WB5). The boundaries for potential contour map visualization are ± 5 kT/e. The cap-4 molecule (shown in sticks) is positioned on LmEIF4E1, based on the superposition of TcEIF4E5-cap-4 structure. The regions corresponding to the connections between β1–β2, β3–β4 and β5–β6 strands (S1–S2, S3–S4 and S5–S6) are indicated. Electrostatic potential was calculated using the Adaptive Poisson–Boltzmann Solver through the software Chimera .

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Software

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Microscale thermophoresis analysis of T. cruzi EIF4E5 binding to mRNA cap analogues. TcEIF4E5 presented low affinity to m7GTP and cap-4 (light and dark blue, K d = 21 ± 7 and 110 ± 33 μM, respectively). Deletion of the C-terminal region abolishes the interaction (TcEIF4E5-ΔC, dark and light green).

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Microscale Thermophoresis, Binding Assay

Journal: Nucleic Acids Research

Article Title: Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4

doi: 10.1093/nar/gkz339

Figure Lengend Snippet: Structural superposition of TcEIF4E5-cap-4 (purple), human eIF4E1 (green) and Schistosoma mansoni eIF4E1 (salmon) in complex with m 7 GTPA (PDB: 1IPB and 3HXG, respectively). The ligands are represented in sticks and identified by the positions of the second base. Cap-1 (pink) is superimposed. The residues forming the m 7 G sandwich are represented in sticks and numbered according to TcEIF4E5 sequence. Human and Schistosoma eIF4E1 C-terminal regions, structured upon binding of a dinucleotide, are indicated. TcEIF4E5 model lacks C-terminal residues 187–200. The last residue built in TcEIF4E5 model (F186) is shown in sticks.

Article Snippet: X-ray diffraction data from TcEIF4E5-SeMet crystals were collected at the PROXIMA 2 beam line of the Synchrotron SOLEIL using an EIGER X 9M detector (Dectris) at the Se-absorption wedge wavelength (0.97830 Å).

Techniques: Sequencing, Binding Assay

Journal: Nature structural & molecular biology

Article Title: Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis

doi: 10.1038/nsmb.3428

Figure Lengend Snippet: Data collection and refinement statistics.

Article Snippet: Initial phases were determined from a SAD data set collected on a SeMet substituted crystal at beamline X25 at the NSLS at Brookhaven National Laboratory to 3.0 Å resolution (λ=0.979 Å).

Techniques: