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10yh

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

Method: ELECTRON MICROSCOPY D_max: 140.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10yh
deposition_date	2026-02-12
title	DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite)
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	43.15 Å
rg_electron	41.80 Å
i0	997126000.00
molecular_weight	199350.0 kDa
excluded_volume	224260 Å³
envelope_volume	340920 Å³
shell_volume	68155 Å³
envelope_diameter	142.7 Å
shell_rg	47.14 Å
envelope_rg	41.25 Å
shape_rg	41.71 Å
total_rg	42.23 Å
total_atoms	13642
n_residues	1250
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	140.2 Å
rg_real	43.06 Å
rg_real_error	1.56 Å
i0_real	9.9710e+08
i0_real_error	1.8290e+07
rg_reciprocal	43.15 Å
i0_reciprocal	997200000.0000
total_estimate	0.8820
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.5 Å
skewness	0.255
kurtosis	-0.412
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	71180000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.810

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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	13642

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-H
formula_weight	11692.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLP

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 1)
formula_weight	4623.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGGATGTATATAT

Entity 7 polymer

description	601 K strand (damaged strand 2)
formula_weight	40942.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

CTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

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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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.90 Å
resolution_method	—
num_particles	74600

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

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

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)