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Yorodumi- PDB-9y3p: Eukaryotic translation initiation factor 2-B in its apo form (act... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9y3p | ||||||||||||||||||||||||
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| Title | Eukaryotic translation initiation factor 2-B in its apo form (active-state) | ||||||||||||||||||||||||
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Keywords | TRANSLATION / Guanine nucleotide exchange factor / GEF / initiation | ||||||||||||||||||||||||
| Function / homology | Function and homology informationeukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / ovarian follicle development / response to glucose / positive regulation of translational initiation ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / ovarian follicle development / response to glucose / positive regulation of translational initiation / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / hippocampus development / central nervous system development / translational initiation / response to peptide hormone / T cell receptor signaling pathway / regulation of translation / response to heat / positive regulation of apoptotic process / GTP binding / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||
Authors | Dalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A. | ||||||||||||||||||||||||
| Funding support | United States, 1items
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Citation | Journal: Nat Chem Biol / Year: 2026Title: Allosteric disordering of eIF2B regulates the integrated stress response. Authors: Udit Dalwadi / Advait Subramanian / Aniliese Deal / Julia E Conrad / Tamara Nadjsombati / Meera Venkatesh / Morgane Boone / Pascal F Egea / Lingjie He / Nimit Jain / D John Lee / Yuwei Liu / ...Authors: Udit Dalwadi / Advait Subramanian / Aniliese Deal / Julia E Conrad / Tamara Nadjsombati / Meera Venkatesh / Morgane Boone / Pascal F Egea / Lingjie He / Nimit Jain / D John Lee / Yuwei Liu / Lucas C Reineke / Kazuki Saito / Nathaniel Talledge / Hannah Toutkoushian / Maxence Le Vasseur / Francesca Zappa / Raoul J de Groot / Diego Acosta-Alvear / Christopher P Arthur / Jodi Nunnari / Susan Marqusee / Rosalie E Lawrence / Mauro Costa-Mattioli / James J Crawford / Frank J M van Kuppeveld / Tristan I Croll / Peter Walter / Adam Frost / ![]() Abstract: The ternary complex, composed of eIF2, GTP and initiator methionyl-tRNA, delivers the first amino acid to the ribosome to initiate protein synthesis. Eukaryotic initiation factor 2B (eIF2B) catalyzes ...The ternary complex, composed of eIF2, GTP and initiator methionyl-tRNA, delivers the first amino acid to the ribosome to initiate protein synthesis. Eukaryotic initiation factor 2B (eIF2B) catalyzes GDP to GTP exchange on eIF2, thereby setting the ternary complex level. Stress-induced phosphorylation converts eIF2 from the substrate of eIF2B into an inhibitor (eIF2-P). This conversion reduces ternary complex levels and induces the integrated stress response (ISR). Here we chart an allosteric axis running through eIF2B, revealing the importance of an α-helix in its β-subunit, the 'latch-helix', that hooks onto the α-subunit to induce eIF2B activity. eIF2-P binding promotes latch-helix unhooking, opening eIF2B, which inhibits its activity. Convergently evolved viral proteins stabilize this latch-helix-binding active state of eIF2B. Using these insights, we generated ISR-activating compounds that stabilize eIF2B in its inhibited, unlatched state. Our study thus highlights how long-range eIF2B allostery can be pharmacologically manipulated to sustain or attenuate the ISR. | ||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9y3p.cif.gz | 909.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9y3p.ent.gz | 579.9 KB | Display | PDB format |
| PDBx/mmJSON format | 9y3p.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/9y3p ftp://data.pdbj.org/pub/pdb/validation_reports/y3/9y3p | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 72462MC ![]() 9y3qC ![]() 9y3tC ![]() 9y3uC ![]() 9y3vC ![]() 9y4bC ![]() 9y4wC ![]() 9y5rC ![]() 9y5sC ![]() 9y5tC ![]() 9y5uC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-Translation initiation factor eIF2B subunit ... , 5 types, 8 molecules ABCDEFIJ
| #1: Protein | Mass: 51385.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B5, EIF2BE / Production host: ![]() #2: Protein | Mass: 38395.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: ![]() #3: Protein | | Mass: 39617.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: ![]() #4: Protein | | Mass: 39489.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: ![]() #6: Protein | Mass: 49304.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B3 / Production host: ![]() |
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-Protein , 1 types, 2 molecules GH
| #5: Protein | Mass: 33754.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B1, EIF2BA / Production host: ![]() |
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-Non-polymers , 3 types, 15 molecules 




| #7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | N |
-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: Eukaryotic translation initiation factor 2B / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT | |||||||||||||||||||||||||
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| Molecular weight | Value: 0.521758 MDa / Experimental value: NO | |||||||||||||||||||||||||
| Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
| Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
| Buffer solution | pH: 7.4 Details: 20 mM HEPES KOH pH 7.4, 200 mM KCl, 5 mM MgCl2, 1 mM TCEP | |||||||||||||||||||||||||
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| Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
| Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
| Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
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Electron microscopy imaging
| Microscopy | Model: TFS GLACIOS |
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| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 18826 |
| EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 10 eV |
| Image scans | Width: 4096 / Height: 4096 |
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Processing
| EM software |
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 890578 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60012 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | PDB-ID: 7L7G Accession code: 7L7G / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement | Resolution: 2.9→457.523 Å / Num. reflection obs: 8225149 / Average fsc work: 0.789 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 64.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
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| LS refinement shell |
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About Yorodumi



Homo sapiens (human)
United States, 1items
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