7RPX

Archaeal DNA ligase and heterotrimeric PCNA in complex with end-joined DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase.

Sverzhinsky, A.Tomkinson, A.E.Pascal, J.M.

(2022) Structure 30: 371

  • DOI: 10.1016/j.str.2021.11.002
  • Primary Citation of Related Structures:  
    7RPO, 7RPW, 7RPX

  • PubMed Abstract: 
  • DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break ...

    DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break. The cryo-EM structures highlight a continuous DNA-binding surface formed between DNA ligase and PCNA that supports the distorted conformation of the DNA break undergoing repair and contributes to PCNA stimulation of DNA ligation. DNA ligase is conformationally flexible within the complex, with its domains fully ordered only when encircling the repaired DNA to form a stacked ring structure with PCNA. The structures highlight DNA ligase structural transitions while docked on PCNA, changes in DNA conformation during ligation, and the potential for DNA ligase domains to regulate PCNA accessibility to other repair factors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada. Electronic address: john.pascal@umontreal.ca.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 1A258Saccharolobus solfataricusMutation(s): 0 
Gene Names: pcn1pcnA-likeSSO0397C41_008
UniProt
Find proteins for P57766 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Go to UniProtKB:  P57766
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UniProt GroupP57766
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 2B245Saccharolobus solfataricusMutation(s): 0 
Gene Names: pcn2pcnA-2SSO1047
UniProt
Find proteins for Q97Z84 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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UniProt GroupQ97Z84
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 3C252Saccharolobus solfataricusMutation(s): 0 
Gene Names: pcn3pcnA-1SSO0405C41_016
UniProt
Find proteins for P57765 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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UniProt GroupP57765
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligaseF [auth E]621Saccharolobus solfataricusMutation(s): 0 
Gene Names: ligSSO0189
EC: 6.5.1.1
UniProt
Find proteins for Q980T8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 4
MoleculeChainsLengthOrganismImage
End-joined DNAD [auth X]47Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Template strand DNAE [auth Z]47Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth X],
H [auth E],
I [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)United StatesRGPIN-2015-05776
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA92584

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2022-03-16
    Changes: Database references