+Open data
-Basic information
Entry | Database: PDB / ID: 6jlz | |||||||||
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Title | P-eIF2a - eIF2B complex | |||||||||
Components |
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Keywords | TRANSLATION / Translation Initiation | |||||||||
Function / homology | Function and homology information Recycling of eIF2:GDP / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / : / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / formation of translation preinitiation complex ...Recycling of eIF2:GDP / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / : / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / formation of translation preinitiation complex / guanyl-nucleotide exchange factor complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of TORC1 signaling / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / translational initiation / cytoplasmic stress granule / ribosome binding / ribosome / RNA binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.35 Å | |||||||||
Authors | Kashiwagi, K. / Ito, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Science / Year: 2019 Title: Structural basis for eIF2B inhibition in integrated stress response. Authors: Kazuhiro Kashiwagi / Takeshi Yokoyama / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Mikako Shirouzu / Takuhiro Ito / Abstract: A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation ...A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5'-triphosphate-dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo-electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jlz.cif.gz | 807.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jlz.ent.gz | 667.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jlz_validation.pdf.gz | 580.6 KB | Display | wwPDB validaton report |
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Full document | 6jlz_full_validation.pdf.gz | 679.4 KB | Display | |
Data in XML | 6jlz_validation.xml.gz | 142.7 KB | Display | |
Data in CIF | 6jlz_validation.cif.gz | 192.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/6jlz ftp://data.pdbj.org/pub/pdb/validation_reports/jl/6jlz | HTTPS FTP |
-Related structure data
Related structure data | 9840C 9841C 9842C 6jlyC 6k71C 6k72C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABLM
#1: Protein | Mass: 37817.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tif221, SPCC11E10.07c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USP0 #6: Protein | Mass: 34843.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Escherichia coli (E. coli) / References: UniProt: P20459 |
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-Probable translation initiation factor eIF-2B subunit ... , 4 types, 8 molecules CDEFGHIJ
#2: Protein | Mass: 43897.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tif222, SPAC343.14c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT76 #3: Protein | Mass: 50551.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tif223, SPAC4D7.09 / Production host: Escherichia coli (E. coli) / References: UniProt: P56288 #4: Protein | Mass: 51652.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tif224, SPAC21E11.06 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09924 #5: Protein | Mass: 76413.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tif225, SPAC8C9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: P56287 |
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-Non-polymers , 1 types, 12 molecules
#7: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, sodium citrate, PEG 4000, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 140658 / % possible obs: 99.7 % / Redundancy: 3.5 % / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.35→3.55 Å |
-Processing
Software |
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Refinement | Resolution: 3.35→49.313 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / Phase error: 28.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→49.313 Å
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Refine LS restraints |
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LS refinement shell |
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