10YI | pdb_000010yi

XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite)

• PDB DOI: https://doi.org/10.2210/pdb10YI/pdb
• EM Map EMD-75530: EMDB EMDataResource
• NAKB: 10YI

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2026-02-12 Released: 2026-03-18 
• Deposition Author(s): Boesch, D.J., Weaver, T.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of nick ligation in the nucleosome by DNA Ligase III alpha

Boesch, D.J., Martin, N.I., Kontor, C.A., Nguyen, A.G., Tomkinson, A.E., Van Houten, B., Gillet, N., Bignon, E., Whitaker, A.M., Weaver, T.M.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-77207-7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 199.98 kDa 
• Atom Count: 13,642 
• Modeled Residue Count: 1,250 
• Deposited Residue Count: 1,256 
• Unique protein chains: 5
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	97	Homo sapiens	Mutation(s): 1  Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	80	Homo sapiens	Mutation(s): 0  Gene Names:  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
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-H	C, G	107	Homo sapiens	Mutation(s): 0  Gene Names: H2AC12, HIST1H2AH, HIST1H2AI
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KK5 (Homo sapiens) Explore Q96KK5  Go to UniProtKB:  Q96KK5
PHAROS:  Q96KK5 GTEx:  ENSG00000274997

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-M	D, H	93	Homo sapiens	Mutation(s): 0  Gene Names: H2BC14, H2BFE, HIST1H2BM
UniProt & NIH Common Fund Data Resources
Find proteins for Q99879 (Homo sapiens) Explore Q99879  Go to UniProtKB:  Q99879
PHAROS:  Q99879 GTEx:  ENSG00000273703

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase 3	L	208	Homo sapiens	Mutation(s): 0  Gene Names: LIG3 EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49916 (Homo sapiens) Explore P49916  Go to UniProtKB:  P49916
PHAROS:  P49916 GTEx:  ENSG00000005156

Entity ID: 5
Molecule	Chains	Length	Organism	Image
601 I strand (non-damaged strand)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
601 J strand (damaged strand 1)	J	15	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
601 K strand (damaged strand 2)	K	132	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	M [auth L]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Boesch, D.J., Weaver, T.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references