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- PDB-9cqc: The ligation complex like in the NHEJ pathway -

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Entry
Database: PDB / ID: 9cqc
TitleThe ligation complex like in the NHEJ pathway
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (34-MER)
  • DNA (35-MER)
  • DNA (38-MER)
  • DNA (40-MER)
  • DNA ligase 4
  • DNA repair protein XRCC4
  • Non-homologous end-joining factor 1
  • Protein PAXX
KeywordsLIGASE/TRANSFERASE/DNA / NHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / LIGASE-TRANSFERASE-DNA complex
Function / homology
Function and homology information


T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / pro-B cell differentiation / DNA ligase IV complex / positive regulation of ligase activity / DNA ligase activity / DNA-dependent protein kinase complex / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex ...T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / pro-B cell differentiation / DNA ligase IV complex / positive regulation of ligase activity / DNA ligase activity / DNA-dependent protein kinase complex / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex / DNA ligase (ATP) / negative regulation of t-circle formation / DNA end binding / DNA ligase (ATP) activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / V(D)J recombination / nonhomologous end joining complex / nucleotide-excision repair, DNA gap filling / cellular response to X-ray / isotype switching / cellular response to lithium ion / regulation of smooth muscle cell proliferation / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / protein localization to site of double-strand break / nuclear telomere cap complex / single strand break repair / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / cellular hyperosmotic salinity response / somatic stem cell population maintenance / protein localization to chromosome, telomeric region / DNA biosynthetic process / 2-LTR circle formation / response to ionizing radiation / telomeric repeat DNA binding / ligase activity / T cell differentiation / DNA 3'-5' helicase / 5'-deoxyribose-5-phosphate lyase activity / chromosome organization / response to X-ray / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / condensed chromosome / site of DNA damage / B cell differentiation / DNA polymerase binding / response to gamma radiation / activation of innate immune response / telomere maintenance / cyclin binding / DNA helicase activity / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to ionizing radiation / central nervous system development / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / cell population proliferation / protein-DNA complex / base-excision repair / establishment of integrated proviral latency / double-strand break repair via nonhomologous end joining / positive regulation of fibroblast proliferation / enzyme activator activity / in utero embryonic development / fibrillar center / T cell differentiation in thymus / neuron apoptotic process / double-strand break repair / site of double-strand break / transcription regulator complex / scaffold protein binding / double-stranded DNA binding / DNA recombination / secretory granule lumen / negative regulation of neuron apoptotic process / molecular adaptor activity / ficolin-1-rich granule lumen / damaged DNA binding / protein-macromolecule adaptor activity / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / DNA damage response
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / DNA ligase IV domain / DNA ligase IV ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / Ku70, bridge and pillars domain superfamily / : / Ku70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / Ku, C-terminal / Ku, C-terminal domain superfamily / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / ATP-dependent DNA ligase family profile. / SPOC-like, C-terminal domain superfamily / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SAP domain superfamily / DNA repair protein XRCC4-like, C-terminal / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / von Willebrand factor (vWF) type A domain / BRCT domain superfamily / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-DZ4 / DNA / DNA (> 10) / DNA repair protein Ku70 / DNA repair protein Ku80 / DNA ligase 4 / DNA repair protein XRCC4 / Protein PAXX / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, J. / Liu, L. / Gellert, M. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2025
Title: Dynamic assemblies and coordinated reactions of non-homologous end joining.
Authors: Lan Liu / Jun Li / Metztli Cisneros-Aguirre / Arianna Merkell / Jeremy M Stark / Martin Gellert / Wei Yang /
Abstract: Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA ...Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA polymerase μ and ligase IV (LIG4) engaged in gap filling and end joining. These reactions take place in a flexible ω-shaped framework composed of XRCC4 and XLF. Two broken DNA ends, each encircled by Ku70-Ku80 internally, are docked onto the ω frame, mediated by LIG4. DNA polymerase and ligase attached to each ω arm repair only one broken strand of a defined polarity; the final steps of NHEJ requires coordination and toggling of a pair of such enzymes. The facilitators XLF and PAXX additively stimulate NHEJ reactions. As DNA-end sensor and protector, LIG4 replaces DNA-PKcs for end joining and bridges the two DNA ends for polymerase to fill remaining gaps. These assemblies present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.
History
DepositionJul 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jun 25, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
C: Non-homologous end-joining factor 1
D: DNA repair protein XRCC4
E: DNA repair protein XRCC4
F: DNA ligase 4
G: Protein PAXX
H: Protein PAXX
I: DNA (38-MER)
J: DNA (40-MER)
K: DNA (34-MER)
L: DNA (35-MER)
a: X-ray repair cross-complementing protein 6
b: X-ray repair cross-complementing protein 5
c: Non-homologous end-joining factor 1
d: DNA repair protein XRCC4
e: DNA repair protein XRCC4
f: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)855,32619
Polymers854,83618
Non-polymers4901
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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X-ray repair cross-complementing protein ... , 2 types, 4 molecules AaBb

#1: Protein X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 70198.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein X-ray repair cross-complementing protein 5


Mass: 82812.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P13010

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Protein , 4 types, 10 molecules CcDEdeFfGH

#3: Protein Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 33625.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Homo sapiens (human) / References: UniProt: Q9H9Q4
#4: Protein
DNA repair protein XRCC4 / X-ray repair cross-complementing protein 4


Mass: 38337.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13426
#5: Protein DNA ligase 4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 104378.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P49917, DNA ligase (ATP)
#6: Protein Protein PAXX / Paralog of XRCC4 and XLF / XRCC4-like small protein


Mass: 23282.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAXX, C9orf142, XLS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUH6

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DNA chain , 4 types, 4 molecules IJKL

#7: DNA chain DNA (38-MER)


Mass: 20737.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#8: DNA chain DNA (40-MER)


Mass: 20795.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#9: DNA chain DNA (34-MER)


Mass: 15865.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#10: DNA chain DNA (35-MER)


Mass: 15493.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#11: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ligation complex like in the NHEJ pathway / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.854 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133163
Details: The resolution is calculated by postprocess in RELION based on the composite half maps generated by phenix.combine_focused_maps.
Symmetry type: POINT
RefinementCross valid method: NONE

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