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- PDB-7nzm: Cryo-EM structure of pre-dephosphorylation complex of phosphoryla... -
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Basic information
Entry | Database: PDB / ID: 7nzm | ||||||
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Title | Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I) | ||||||
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![]() | HYDROLASE / holophosphatase / PP1 / PPP1R15A / phosphorylated eIF2alpha | ||||||
Function / homology | ![]() fatty acid derivative binding / positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / positive regulation of peptidyl-serine dephosphorylation / deoxyribonuclease I / regulation of translation in response to endoplasmic reticulum stress ...fatty acid derivative binding / positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / positive regulation of peptidyl-serine dephosphorylation / deoxyribonuclease I / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / protein phosphatase type 1 complex / glial limiting end-foot / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / PTW/PP1 phosphatase complex / Recycling of eIF2:GDP / negative regulation of protein dephosphorylation / PERK-mediated unfolded protein response / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / peptidyl-serine dephosphorylation / regulation of translational initiation in response to stress / neutrophil activation involved in immune response / protein localization to endoplasmic reticulum / deoxyribonuclease I activity / protein phosphatase regulator activity / protein phosphatase 1 binding / eukaryotic 48S preinitiation complex / DNA catabolic process / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cytoskeletal motor activator activity / myosin phosphatase activity / negative regulation of phosphoprotein phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / detection of maltose stimulus / maltose transport complex / negative regulation of PERK-mediated unfolded protein response / protein-serine/threonine phosphatase / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / entrainment of circadian clock by photoperiod / protein phosphatase activator activity / phosphatase activity / filamentous actin / actin filament bundle / carbohydrate transport / positive regulation of phosphoprotein phosphatase activity / phosphoprotein phosphatase activity / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / Response of EIF2AK4 (GCN2) to amino acid deficiency / carbohydrate transmembrane transporter activity / skeletal muscle myofibril / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / maltose binding / actin monomer binding / maltose transport / maltodextrin transmembrane transport / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / skeletal muscle fiber development / stress granule assembly / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / stress fiber / titin binding / translational initiation / translation initiation factor activity / cellular response to amino acid starvation / actin filament polymerization / response to endoplasmic reticulum stress / ATP-binding cassette (ABC) transporter complex / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / cell chemotaxis / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian regulation of gene expression / ABC-family proteins mediated transport / PKR-mediated signaling / regulation of circadian rhythm / cytoplasmic stress granule / calcium-dependent protein binding / cellular response to UV / positive regulation of canonical Wnt signaling pathway / lamellipodium / ribosome binding / nuclear envelope / actin binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||
![]() | Yan, Y. / Hardwick, S. / Ron, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Higher-order phosphatase-substrate contacts terminate the integrated stress response. Authors: Yahui Yan / Heather P Harding / David Ron / ![]() Abstract: Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally ...Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally affecting flexible access of the phosphopeptide to the active site. However, catalytic efficiency of holophosphatases towards their phosphoprotein substrates remains unexplained. Here we present a cryo-EM structure of the tripartite PP1c-PPP1R15A-G-actin holophosphatase that terminates signaling in the mammalian integrated stress response (ISR) in the pre-dephosphorylation complex with its substrate, translation initiation factor 2α (eIF2α). G-actin, whose essential role in eIF2α dephosphorylation is supported crystallographically, biochemically and genetically, aligns the catalytic and regulatory subunits, creating a composite surface that engages the N-terminal domain of eIF2α to position the distant phosphoserine-51 at the active site. Substrate residues that mediate affinity for the holophosphatase also make critical contacts with eIF2α kinases. Thus, a convergent process of higher-order substrate recognition specifies functionally antagonistic phosphorylation and dephosphorylation in the ISR. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 221.8 KB | Display | ![]() |
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PDB format | ![]() | 174.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 51.4 KB | Display | |
Data in CIF | ![]() | 76.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12665MC ![]() 7nxvC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 5 types, 5 molecules EBADC
#1: Protein | Mass: 21817.863 Da / Num. of mol.: 1 / Mutation: phosphorylated Ser51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 33647.621 Da / Num. of mol.: 1 / Mutation: D64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P62139, protein-serine/threonine phosphatase |
#3: Protein | Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 49169.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PPP1R15A, GADD34, malE, b4034, JW3994 / Strain: K12 / Production host: ![]() ![]() |
-Sugars , 1 types, 1 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#7: Chemical | ChemComp-MN / |
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#8: Chemical | ChemComp-ATP / |
-Details
Has ligand of interest | Y |
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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: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin) Type: COMPLEX Details: One copy of each component was present in the complex: phosphorylated eIF2alpha_2-187, PP1A_D64A, PPP1R15A_553-624, G-actin and DNase I. The full complex was purified by size exclusion chromatography. Entity ID: #1-#5 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.181 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: 0.22mM Triton X-100 was added into the solution before plunging. | ||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Details: current 25mA at Pelco EasiGLOW / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1 | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: 130000 X / Nominal defocus max: -2800 nm / Nominal defocus min: -1000 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: 46.84 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4025 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
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Processing
EM software |
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CTF correction | Details: Warp estimated the CTF parameters and passed them on to CryoSPARC to perform CTF correction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 132495 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60413 / Details: non-uniform refinement / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 47 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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