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- PDB-10yh: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 ... -

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Basic information

Entry
Database: PDB / ID: 10yh
TitleDNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite)
Components
  • 601 I strand (non-damaged strand)
  • 601 J strand (damaged strand 1)
  • 601 K strand (damaged strand 2)
  • DNA ligase 3
  • Histone H2A type 1-H
  • Histone H2B type 1-M
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / DNA Ligase IIIa / DNA Repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway / mitochondrial DNA repair / DNA biosynthetic process / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / base-excision repair, gap-filling / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Gap-filling DNA repair synthesis and ligation in GG-NER / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / mitochondrion organization / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / G2/M DNA damage checkpoint / base-excision repair / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Metalloprotease DUBs / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / Gap-filling DNA repair synthesis and ligation in TC-NER / structural constituent of chromatin / UCH proteinases / nucleosome / double-strand break repair / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / gene expression / chromosome, telomeric region / Ub-specific processing proteases / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / cell division / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / 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 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / DNA ligase, ATP-dependent, conserved site / Zinc finger, PARP-type / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA (> 100) / DNA ligase 3 / Histone H4 / Histone H3.2 / Histone H2A type 1-H / Histone H2B type 1-M
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBoesch, D.J. / Weaver, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6
Authors: Boesch, D.J. / Weaver, T.M.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1-H
D: Histone H2B type 1-M
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1-H
H: Histone H2B type 1-M
I: 601 I strand (non-damaged strand)
J: 601 J strand (damaged strand 1)
K: 601 K strand (damaged strand 2)
L: DNA ligase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,97613
Polymers199,62912
Non-polymers3471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHL

#1: Protein Histone H3.2 / H3-clustered histone 13 / H3-clustered histone 14 / H3-clustered histone 15 / Histone H3/m / Histone H3/o


Mass: 11385.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
Production host: Escherichia coli (E. coli) / References: UniProt: Q71DI3
#2: Protein Histone H4


Mass: 9123.692 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-H / H2A-clustered histone 12 / Histone H2A/s


Mass: 11692.677 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC12, HIST1H2AH, HIST1H2AI / Production host: Escherichia coli (E. coli) / References: UniProt: Q96KK5
#4: Protein Histone H2B type 1-M / Histone H2B.e / H2B/e


Mass: 10336.800 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC14, H2BFE, HIST1H2BM / Production host: Escherichia coli (E. coli) / References: UniProt: Q99879
#8: Protein DNA ligase 3 / DNA ligase III / Polydeoxyribonucleotide synthase [ATP] 3


Mass: 23847.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P49916, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules IJK

#5: DNA chain 601 I strand (non-damaged strand)


Mass: 45138.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain 601 J strand (damaged strand 1)


Mass: 4623.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain 601 K strand (damaged strand 2)


Mass: 40942.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74600 / Symmetry type: POINT

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