8BOT image
Deposition Date 2022-11-15
Release Date 2023-06-28
Last Version Date 2023-08-16
Entry Detail
PDB ID:
8BOT
Title:
Cryo-EM structure of NHEJ supercomplex(trimer)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
7.76 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (24-MER)
Chain IDs:Q (auth: D)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (24-MER)
Chain IDs:R (auth: E)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-dependent protein kinase catalytic subunit
Gene (Uniprot):PRKDC
Chain IDs:I (auth: F), N (auth: A), S
Chain Length:4128
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:X-ray repair cross-complementing protein 6
Gene (Uniprot):XRCC6
Chain IDs:J (auth: G), O (auth: B), T
Chain Length:609
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:X-ray repair cross-complementing protein 5
Gene (Uniprot):XRCC5
Chain IDs:K (auth: H), P (auth: C), U
Chain Length:732
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (28-MER)
Chain IDs:L (auth: I), V
Chain Length:28
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (27-MER)
Chain IDs:M (auth: J), W
Chain Length:27
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA repair protein XRCC4
Gene (Uniprot):XRCC4
Chain IDs:A (auth: K), B (auth: L), D (auth: N), E (auth: O)
Chain Length:336
Number of Molecules:4
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA ligase 4
Gene (Uniprot):LIG4
Chain IDs:C (auth: M), F (auth: P)
Chain Length:911
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-homologous end-joining factor 1
Gene (Uniprot):NHEJ1
Chain IDs:G (auth: Q), H (auth: R), X, Y
Chain Length:299
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ.
Structure 31 895 ? (2023)
PMID: 37311458 DOI: 10.1016/j.str.2023.05.013

Abstact

The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ultimately lead to diseases including cancer. Non-homologous end joining (NHEJ) is one of two core mechanisms utilized to repair DSBs. DNA-PK is a key component in this process and has recently been shown to form alternate long-range synaptic dimers. This has led to the proposal that these complexes can be formed before transitioning to a short-range synaptic complex. Here we present cryo-EM data representing an NHEJ supercomplex consisting of a trimer of DNA-PK in complex with XLF, XRCC4, and DNA Ligase IV. This trimer represents a complex of both long-range synaptic dimers. We discuss the potential role of the trimeric structure, and possible higher order oligomers, as structural intermediates in the NHEJ mechanism, or as functional DNA repair centers.

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