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- PDB-9cq3: The gap-filling complex with Pol mu engaged in the NHEJ pathway -

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Basic information

Entry
Database: PDB / ID: 9cq3
TitleThe gap-filling complex with Pol mu engaged in the NHEJ pathway
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (34-MER)
  • DNA (37-MER)
  • DNA (38-MER)
  • DNA (42-MER)
  • DNA ligase 4
  • DNA repair protein XRCC4
  • DNA-directed DNA/RNA polymerase mu
  • Non-homologous end-joining factor 1
  • Protein PAXX
KeywordsLIGASE/TRANSFERASE/DNA / NHEJ / DNA gap / fill-in synthesis / ligation / XLF / PAXX / Polymerase mu / 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 double-strand break attachment to nuclear envelope / DNA ligase (ATP) / 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 double-strand break attachment to nuclear envelope / DNA ligase (ATP) / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA ligase (ATP) activity / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nucleotide-excision repair, DNA gap filling / isotype switching / nonhomologous end joining complex / V(D)J recombination / cellular response to X-ray / regulation of smooth muscle cell proliferation / somatic stem cell population maintenance / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / single strand break repair / IRF3-mediated induction of type I IFN / cellular hyperosmotic salinity response / positive regulation of neurogenesis / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / chromosome organization / response to X-ray / DNA biosynthetic process / protein localization to chromosome, telomeric region / ligase activity / 2-LTR circle formation / response to ionizing radiation / telomeric repeat DNA binding / T cell differentiation / DNA 3'-5' helicase / T cell differentiation in thymus / 5'-deoxyribose-5-phosphate lyase activity / neuron apoptotic process / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / B cell differentiation / condensed chromosome / DNA polymerase binding / response to gamma radiation / in utero embryonic development / activation of innate immune response / positive regulation of fibroblast proliferation / 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 / site of DNA damage / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / establishment of integrated proviral latency / base-excision repair / double-strand break repair via nonhomologous end joining / fibrillar center / cell population proliferation / enzyme activator activity / double-strand break repair / site of double-strand break / negative regulation of neuron apoptotic process / transcription regulator complex / DNA recombination / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA-directed DNA polymerase / ficolin-1-rich granule lumen / damaged DNA binding / DNA-directed DNA polymerase activity / molecular adaptor activity / chromosome, telomeric region / protein-macromolecule adaptor activity / transcription cis-regulatory region binding / innate immune response / chromosome / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / 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 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / ATP-dependent DNA ligase AMP-binding site. / DNA-directed DNA/RNA polymerase mu / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / DNA ligase, ATP-dependent, conserved site / Ku70/Ku80 N-terminal alpha/beta domain / ATP-dependent DNA ligase family profile. / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SPOC-like, C-terminal domain superfamily / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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 / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / breast cancer carboxy-terminal domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase beta-like, N-terminal domain / DNA polymerase lambda lyase domain superfamily / Helix-hairpin-helix domain / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / BRCT domain profile. / BRCT domain / von Willebrand factor (vWF) type A domain / BRCT domain superfamily / von Willebrand factor, type A / Nucleotidyltransferase superfamily / 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 / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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
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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
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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 (42-MER)
K: DNA (34-MER)
L: DNA (37-MER)
M: DNA-directed DNA/RNA polymerase mu
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
m: DNA-directed DNA/RNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)969,32223
Polymers968,78320
Non-polymers5393
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 , 5 types, 12 molecules CcDEdeFfGHMm

#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 / Cell line (production host): HEK293T / 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
#11: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 56973.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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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 (42-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 (37-MER)


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

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Non-polymers , 2 types, 3 molecules

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: 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: A gap-filling complex with Pol mu engaged / Type: COMPLEX / Entity ID: #1-#5, #7-#11 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.967 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 891208
Details: The resolution is calculated by the postprocess in RELION with the two composite half maps. The composite maps were generated by Phenix.combine_focused_maps
Symmetry type: POINT
RefinementCross valid method: NONE

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