7OPL

CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase alpha-primase.

Kilkenny, M.L.Veale, C.E.Guppy, A.Hardwick, S.W.Chirgadze, D.Y.Rzechorzek, N.J.Maman, J.D.Pellegrini, L.

(2022) Protein Sci 31: 333-344

  • DOI: https://doi.org/10.1002/pro.4220
  • Primary Citation of Related Structures:  
    7OPL

  • PubMed Abstract: 

    The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense current scrutiny to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated. Recent proteomic screens of the interactions between viral and host proteins have identified the human proteins targeted by SARS-CoV-2. The DNA polymerase α (Pol α)-primase complex or primosome-responsible for initiating DNA synthesis during genomic duplication-was identified as a target of nonstructural protein 1 (nsp1), a major virulence factor in the SARS-CoV-2 infection. Here, we validate the published reports of the interaction of nsp1 with the primosome by demonstrating direct binding with purified recombinant components and providing a biochemical characterization of their interaction. Furthermore, we provide a structural basis for the interaction by elucidating the cryo-electron microscopy structure of nsp1 bound to the primosome. Our findings provide biochemical evidence for the reported targeting of Pol α by the virulence factor nsp1 and suggest that SARS-CoV-2 interferes with Pol α's putative role in the immune response during the viral infection.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit1,170Homo sapiensMutation(s): 0 
Gene Names: POLA1POLA
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
PHAROS:  P09884
GTEx:  ENSG00000101868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09884
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit B452Homo sapiensMutation(s): 0 
Gene Names: POLA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14181 (Homo sapiens)
Go to UniProtKB:  Q14181
PHAROS:  Q14181
GTEx:  ENSG00000014138 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit441Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens)
Go to UniProtKB:  P49642
PHAROS:  P49642
GTEx:  ENSG00000198056 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit509Homo sapiensMutation(s): 0 
Gene Names: PRIM2PRIM2A
UniProt & NIH Common Fund Data Resources
Find proteins for P49643 (Homo sapiens)
Explore P49643 
Go to UniProtKB:  P49643
PHAROS:  P49643
GTEx:  ENSG00000146143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49643
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 1119Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Go to UniProtKB:  P0C6U8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19.1-4122

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Data collection, Database references
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2024-07-17
    Changes: Data collection, Refinement description