7QNZ

human Lig1-DNA-PCNA complex reconstituted in absence of ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing.

Blair, K.Tehseen, M.Raducanu, V.S.Shahid, T.Lancey, C.Rashid, F.Creuhet, R.Hamdan, S.M.De Biasio, A.

(2022) Nat Commun 13: 7833-7833

  • DOI: https://doi.org/10.1038/s41467-022-35475-z
  • Primary Citation of Related Structures:  
    7QNZ, 7QO1, 8B8T

  • PubMed Abstract: 

    During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIP N-term ) and DNA binding domain (PIP DBD ). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIP N-term is released from PCNA and only PIP DBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.


  • Organizational Affiliation

    Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 1919Homo sapiensMutation(s): 0 
Gene Names: LIG1
EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P18858 (Homo sapiens)
Explore P18858 
Go to UniProtKB:  P18858
PHAROS:  P18858
GTEx:  ENSG00000105486 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18858
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
B, C, D
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
GTEx:  ENSG00000132646 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
Oligo19ddCE [auth H]19synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
Oligo13PF [auth I]13synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
Oligo32G [auth J]32synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
H [auth I]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release