7NZM

Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Higher-order phosphatase-substrate contacts terminate the integrated stress response.

Yan, Y.Harding, H.P.Ron, D.

(2021) Nat Struct Mol Biol 28: 835-846

  • DOI: https://doi.org/10.1038/s41594-021-00666-7
  • Primary Citation of Related Structures:  
    7NXV, 7NZM

  • PubMed 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 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.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1A [auth E]186Homo sapiensMutation(s): 0 
Gene Names: EIF2S1EIF2A
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Find proteins for P05198 (Homo sapiens)
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PHAROS:  P05198
GTEx:  ENSG00000134001 
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UniProt GroupP05198
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit294Oryctolagus cuniculusMutation(s): 1 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt
Find proteins for P62139 (Oryctolagus cuniculus)
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UniProt GroupP62139
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle, intermediate formC [auth A]375Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribonuclease-1260Bos taurusMutation(s): 0 
EC: 3.1.21.1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic proteinE [auth C]444Homo sapiensEscherichia coli K-12
This entity is chimeric
Mutation(s): 0 
Gene Names: PPP1R15AGADD34malEb4034JW3994
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Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Find proteins for O75807 (Homo sapiens)
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PHAROS:  O75807
GTEx:  ENSG00000087074 
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UniProt GroupsO75807P0AEX9
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth E]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT 2008/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Data collection, Database references