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- PDB-6qg2: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qg2 | ||||||||||||
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Title | Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A) | ||||||||||||
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![]() | TRANSLATION / integrated stress response / ISR / initiation factors / phosphorylation / eIF2 / eIF2B / tRNAi / GEF / heat domain / eIF2 alpha | ||||||||||||
Function / homology | ![]() negative regulation of cellular response to amino acid starvation / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2B complex / eukaryotic translation initiation factor 2 complex / multi-eIF complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex ...negative regulation of cellular response to amino acid starvation / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2B complex / eukaryotic translation initiation factor 2 complex / multi-eIF complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / guanyl-nucleotide exchange factor complex / positive regulation of cellular response to amino acid starvation / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / regulation of translational initiation / 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 / enzyme regulator activity / translation initiation factor binding / translational initiation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / ribosome binding / ribosome / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.55 Å | ||||||||||||
![]() | Llacer, J.L. / Gordiyenko, Y. / Ramakrishnan, V. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis for the inhibition of translation through eIF2α phosphorylation. Authors: Yuliya Gordiyenko / José Luis Llácer / V Ramakrishnan / ![]() ![]() Abstract: One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of ...One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58-63 with eIF2Bδ leading to a competition with Met-tRNA. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 858.7 KB | Display | ![]() |
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PDB format | ![]() | 679.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 125.7 KB | Display | |
Data in CIF | ![]() | 193.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4545MC ![]() 4543C ![]() 4544C ![]() 4546C ![]() 4547C ![]() 4548C ![]() 6qg0C ![]() 6qg1C ![]() 6qg3C ![]() 6qg5C ![]() 6qg6C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Translation initiation factor eIF-2B subunit ... , 5 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 34062.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCN3, AAS2, TIF221, YKR026C / Production host: ![]() ![]() #2: Protein | Mass: 42621.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCD7, TIF222, YLR291C, L8003.17 / Production host: ![]() ![]() #3: Protein | Mass: 65768.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCD1, TIF223, TRA3, YOR260W / Production host: ![]() ![]() #4: Protein | Mass: 70945.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCD2, TIF224, YGR083C / Production host: ![]() ![]() #5: Protein | Mass: 81249.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCD6, TIF225, YDR211W, YD8142.12, YD8142B.03 / Production host: ![]() ![]() |
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-Eukaryotic translation initiation factor 2 subunit ... , 3 types, 6 molecules KLMNOP
#6: Protein | Mass: 34843.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SUI2, TIF211, YJR007W, J1429 / Production host: ![]() ![]() #7: Protein | Mass: 57942.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCD11, TIF213, YER025W / Production host: ![]() ![]() #8: Protein | Mass: 31631.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SUI3, TIF212, YPL237W / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.837 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil, UltrAuFoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 90 K |
Image recording | Electron dose: 45 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 4523 Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in ...Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in integrating mode 1.1 sec images were recorded (dose 45e-/A2) |
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Processing
Software | Name: REFMAC / Version: 5.8.0180 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: FEI Falcon III | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 633220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119037 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSC | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 4.6→281.4 Å / Cor.coef. Fo:Fc: 0.914 / SU B: 327.13 / SU ML: 3.43 / ESU R: 3.458 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.469 Å2
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Refinement step | Cycle: 1 / Resolution: 4.6→281.4 Å / Total: 37959 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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