9NB9 | pdb_00009nb9

Viral protein DP71L in complex with phosphorylated eIF2alpha (NTD) and protein phosphatase 1A (D64A), stabilized by G-actin/DNAseI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Harnessing the Evolution of Proteostasis Networks to Reverse Cognitive Dysfunction.

Reineke, L.C.Zhu, P.J.Dalwadi, U.Dooling, S.W.Liu, Y.Wang, I.C.Young-Baird, S.Okoh, J.Kuncha, S.K.Zhou, H.Kannan, A.Park, H.Debeaubien, N.A.Croll, T.Lee, D.J.Arthur, C.Dever, T.E.Walter, P.Chen, J.Frost, A.Costa-Mattioli, M.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.02.28.640897
  • Primary Citation of Related Structures:  
    9NB9

  • PubMed Abstract: 

    The integrated stress response (ISR) is a highly conserved network essential for maintaining cellular homeostasis and cognitive function. Here, we investigated how persistent ISR activation impacts cognitive performance, primarily focusing on a PPP1R15B R658C genetic variant associated with intellectual disability. By generating a novel mouse model that mimics this human condition, we revealed that this variant destabilizes the PPP1R15B•PP1 phosphatase complex, resulting in chronic ISR activation, impaired protein synthesis, and deficits in long-term memory. Importantly, we found that the cognitive and synaptic deficits in Ppp1r15b R658C mice are directly due to ISR activation. Leveraging insights from evolutionary biology, we characterized DP71L, a viral orthologue of PPP1R15B, through detailed molecular and structural analyses, uncovering its mechanism of action as a potent pan-ISR inhibitor. Remarkably, we found that DP71L not only buffers cognitive decline associated with a wide array of conditions-including Down syndrome, Alzheimer's disease and aging-but also enhances long-term synaptic plasticity and memory in healthy mice. These findings highlight the promise of utilizing evolutionary insight to inform innovative therapeutic strategies.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein DP71LA [auth B]71African swine fever virusMutation(s): 0 
Gene Names: Pret-172
UniProt
Find proteins for P0C753 (African swine fever virus (isolate Warthog/Namibia/Wart80/1980))
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Go to UniProtKB:  P0C753
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UniProt GroupP0C753
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunitB [auth C]330Homo sapiensMutation(s): 1 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
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Go to UniProtKB:  P62136
PHAROS:  P62136
GTEx:  ENSG00000172531 
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UniProt GroupP62136
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleC [auth D]377Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
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UniProt GroupP68135
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribonuclease-1D [auth E]282Bos taurusMutation(s): 0 
EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus)
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UniProt GroupP00639
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1E [auth A]186Homo sapiensMutation(s): 0 
Gene Names: EIF2S1EIF2A
UniProt & NIH Common Fund Data Resources
Find proteins for P05198 (Homo sapiens)
Explore P05198 
Go to UniProtKB:  P05198
PHAROS:  P05198
GTEx:  ENSG00000134001 
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UniProt GroupP05198
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.7
MODEL REFINEMENTServalcat0.4.99
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release