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Yorodumi- PDB-1ipc: CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WI... -
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-Basic information
Entry | Database: PDB / ID: 1ipc | ||||||
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Title | CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP | ||||||
Components | EUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E | ||||||
Keywords | RNA BINDING PROTEIN / Initiation factor / Protein biosynthesis | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. ...Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / Ishikawa, M. / Miura, K. | ||||||
Citation | Journal: BIOCHEM.J. / Year: 2002 Title: Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor ...Title: Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor 4E: biological importance of the C-terminal flexible region Authors: Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / ...Authors: Tomoo, K. / Shen, X. / Okabe, K. / Nozoe, Y. / Fukuhara, S. / Morino, S. / Ishida, T. / Taniguchi, T. / Hasegawa, H. / Terashima, A. / Sasaki, M. / Katsuya, Y. / Kitamura, K. / Miyoshi, H. / Ishikawa, M. / Miura, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ipc.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ipc.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ipc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/1ipc ftp://data.pdbj.org/pub/pdb/validation_reports/ip/1ipc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25130.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEMEX / Production host: Escherichia coli (E. coli) / References: UniProt: P06730 |
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#2: Chemical | ChemComp-MGP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.45 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 21848 / % possible obs: 89.8 % / Rmerge(I) obs: 0.0786 |
-Processing
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Refinement | Resolution: 2→30 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.192 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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