7NFE image
Deposition Date 2021-02-06
Release Date 2021-08-18
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7NFE
Keywords:
DNA BINDING PROTEIN
Title:
Cryo-EM structure of NHEJ super-complex (monomer)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Insect cell expression vector pTIE1
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.29 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7NFE validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit
Gene (Uniprot):PRKDC
Chain IDs:A
Chain Length:4156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P78527 Pfam ID:PF20502, PF08163, PF19704, PF02259, PF00454, PF02260 EC:2.7.11.1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:X-ray repair cross-complementing protein 6
Gene (Uniprot):XRCC6
Chain IDs:B
Chain Length:609
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P12956 Pfam ID:PF03731, PF02735, PF03730, PF02037
Protein Blast
Polymer Type:polypeptide(L)
Molecule:X-ray repair cross-complementing protein 5
Gene (Uniprot):XRCC5
Chain IDs:C
Chain Length:732
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P13010 Pfam ID:PF03731, PF02735, PF03730, PF08785
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP*AP*TP*TP*AP*TP*G)-3')
Chain IDs:I (auth: D)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*AP*G)-3')
Chain IDs:J (auth: E)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-homologous end-joining factor 1
Gene (Uniprot):NHEJ1
Chain IDs:D (auth: F), E (auth: G)
Chain Length:299
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q9H9Q4 Pfam ID:PF09302, PF21928
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA repair protein XRCC4
Gene (Uniprot):XRCC4
Chain IDs:F (auth: H), G (auth: I)
Chain Length:336
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q13426 Pfam ID:PF06632, PF21924, PF21925
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA ligase 4
Gene (Uniprot):LIG4
Chain IDs:H (auth: J)
Chain Length:911
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49917 Pfam ID:PF04675, PF01068, PF04679, PF00533, PF11411 EC:6.5.1.1
Ligand Molecules
NA
Primary Citation
Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Mol.Cell 81 3400 3409 (2021)
PMID: 34352203 DOI: 10.1016/j.molcel.2021.07.005

Abstact

Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair.

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Primary Citation of related structures
7NFE