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10yf

DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite)

Method: ELECTRON MICROSCOPY D_max: 138.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10yf
deposition_date	2026-02-12
title	DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (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	43.04 Å
rg_electron	41.60 Å
i0	996885000.00
molecular_weight	199370.0 kDa
excluded_volume	224340 Å³
envelope_volume	339530 Å³
shell_volume	67799 Å³
envelope_diameter	138.4 Å
shell_rg	47.16 Å
envelope_rg	41.02 Å
shape_rg	41.50 Å
total_rg	42.05 Å
total_atoms	13644
n_residues	1251
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	138.6 Å
rg_real	42.92 Å
rg_real_error	1.12 Å
i0_real	9.9690e+08
i0_real_error	1.9870e+07
rg_reciprocal	43.04 Å
i0_reciprocal	997000000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.7 Å
skewness	0.204
kurtosis	-0.517
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	69050000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.831

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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	11228.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	13644

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGE

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 2-F
formula_weight	10249.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

RKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

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	17352.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGG

Entity 7 polymer

description	601 K strand (damaged strand 2)
formula_weight	28213.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

TTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

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	—

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

DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (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

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)