- EMDB-12665: Cryo-EM structure of pre-dephosphorylation complex of phosphoryla... -
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Basic information
Entry
Database: EMDB / ID: EMD-12665
Title
Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)
Map data
Unsharpened GS-FSC map after corrected FSC-mask auto-tightening from non-uniform refinement in CryoSPARC. The contour level was set when opend in UCSF Chimera.
Sample
Complex: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Protein or peptide: Actin, alpha skeletal muscle, intermediate form
Protein or peptide: Deoxyribonuclease-1
Protein or peptide: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
Ligand: MANGANESE (II) ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information
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 / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex ...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 / 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 / deoxyribonuclease I / 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 / protein localization to endoplasmic reticulum / neutrophil activation involved in immune response / protein phosphatase regulator activity / protein phosphatase 1 binding / deoxyribonuclease I activity / 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 / negative regulation of PERK-mediated unfolded protein response / protein-serine/threonine phosphatase / maltose transport complex / 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 / maltose binding / actin monomer binding / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / maltose transport / maltodextrin transmembrane transport / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / skeletal muscle fiber development / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / stress granule assembly / stress fiber / titin binding / translational initiation / translation initiation factor activity / cellular response to amino acid starvation / actin filament polymerization / ATP-binding cassette (ABC) transporter complex / response to endoplasmic reticulum stress / 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 / PKR-mediated signaling / ABC-family proteins mediated transport / 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
Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain ...Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / S1 domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Ribosomal protein S1-like RNA-binding domain / Bacterial extracellular solute-binding protein / Actin / Actin family / S1 RNA binding domain / Actin / S1 domain / ATPase, nucleotide binding domain / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
Journal: Nat Struct Mol Biol / Year: 2021 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
Deposition
Mar 24, 2021
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Header (metadata) release
Sep 29, 2021
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Map release
Sep 29, 2021
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Update
Oct 20, 2021
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Current status
Oct 20, 2021
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_12665.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Unsharpened GS-FSC map after corrected FSC-mask auto-tightening from non-uniform refinement in CryoSPARC. The contour level was set when opend in UCSF Chimera.
Entire : pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 w...
Entire
Name: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
Components
Complex: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Protein or peptide: Actin, alpha skeletal muscle, intermediate form
Protein or peptide: Deoxyribonuclease-1
Protein or peptide: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
Ligand: MANGANESE (II) ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE
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Supramolecule #1: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 w...
Supramolecule
Name: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 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.
Space: REAL / Protocol: OTHER / Overall B value: 47
Output model
PDB-7nzm: Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)
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