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10ye

DNA Ligase IIIa bound to nucleosome containing a nick at SHL0

Method: ELECTRON MICROSCOPY D_max: 133.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10ye
deposition_date	2026-02-12
title	DNA Ligase IIIa bound to nucleosome containing a nick at SHL0
keywords	Nucleosome, DNA Ligase IIIa, DNA Repair, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	42.84 Å
rg_electron	41.27 Å
i0	1000390000.00
molecular_weight	199910.0 kDa
excluded_volume	224980 Å³
envelope_volume	339890 Å³
shell_volume	67568 Å³
envelope_diameter	135.6 Å
shell_rg	47.62 Å
envelope_rg	40.59 Å
shape_rg	41.17 Å
total_rg	41.76 Å
total_atoms	13681
n_residues	1255
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	133.5 Å
rg_real	42.68 Å
rg_real_error	1.05 Å
i0_real	1.0000e+09
i0_real_error	1.6790e+07
rg_reciprocal	42.84 Å
i0_reciprocal	1001000000.0000
total_estimate	0.8851
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.5 Å
skewness	0.156
kurtosis	-0.586
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	79530000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.675

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Histone H3.2
formula_weight	11385.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	13681

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGER

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	9123.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A type 1
formula_weight	11821.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B type 1-M
formula_weight	10336.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

SRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	601 I strand (non-damaged strand)
formula_weight	45138.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Entity 6 polymer

description	601 J strand (damaged strand)
formula_weight	23630.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCG

Entity 7 polymer

description	601 K strand (damaged strand)
formula_weight	21935.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

CGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Entity 8 polymer

description	DNA ligase 3
formula_weight	23847.9 kDa
ec_number	6.5.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QASLMTPVQPMLAEACKSVEYAMKKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKRHWLKVKKDYL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 9 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	2.50 Å
resolution_method	—
num_particles	463243

fit	/app/data/saxs_computation/0y/10ye/10ye.fit
pddf	/app/data/pr_computation/0y/10ye/10ye.pr.out
profile	/app/data/saxs_computation/0y/10ye/10ye.dat

DNA Ligase IIIa bound to nucleosome containing a nick at SHL0

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)