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

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Basic information

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


FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA ligase (ATP) / DNA end binding ...FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA ligase (ATP) / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / immunoglobulin V(D)J recombination / nucleotide-excision repair, DNA gap filling / regulation of smooth muscle cell proliferation / single strand break repair / V(D)J recombination / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / Cytosolic sensors of pathogen-associated DNA / isotype switching / IRF3-mediated induction of type I IFN / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular response to fatty acid / cellular hyperosmotic salinity response / positive regulation of neurogenesis / response to ionizing radiation / cellular response to lithium ion / DNA biosynthetic process / telomeric DNA binding / 2-LTR circle formation / hematopoietic stem cell proliferation / ligase activity / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / somatic stem cell population maintenance / T cell differentiation / 5'-deoxyribose-5-phosphate lyase activity / ATP-dependent activity, acting on DNA / response to X-ray / positive regulation of protein kinase activity / hematopoietic stem cell differentiation / chromosome organization / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / DNA helicase activity / condensed chromosome / DNA polymerase binding / neurogenesis / telomere maintenance / activation of innate immune response / B cell differentiation / cyclin binding / cellular response to leukemia inhibitory factor / enzyme activator activity / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / small-subunit processome / cellular response to gamma radiation / protein-DNA complex / base-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / fibrillar center / positive regulation of fibroblast proliferation / double-strand break repair / site of double-strand break / T cell differentiation in thymus / double-stranded DNA binding / fibroblast proliferation / scaffold protein binding / secretory granule lumen / neuron apoptotic process / DNA recombination / molecular adaptor activity / transcription regulator complex / negative regulation of neuron apoptotic process / in utero embryonic development / ficolin-1-rich granule lumen / damaged DNA binding / chromosome, telomeric region / cell population proliferation / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex
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 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / DNA ligase, ATP-dependent / Ku70/Ku80 C-terminal arm / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / Ku70/Ku80 C-terminal arm / DNA ligase N terminus / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / 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 / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / SAP domain superfamily / ATP dependent DNA ligase domain / 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 / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-DZ4 / DNA / DNA (> 10) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / 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: Liu, L. / Li, J. / Cisneros-Aguirre, M. / Merkell, A. / Stark, J.M. / Gellert, M. / Yang, W.
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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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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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