SAXSdb — 9uz7

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1. Structure Basics

entry_id	9uz7
deposition_date	2025-05-16
title	Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking
keywords	Histone, Nucleosome, 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	39.61 Å
rg_electron	36.83 Å
i0	801556000.00
molecular_weight	173160.0 kDa
excluded_volume	192470 Å³
envelope_volume	287060 Å³
shell_volume	62938 Å³
envelope_diameter	118.7 Å
shell_rg	44.78 Å
envelope_rg	36.34 Å
shape_rg	36.66 Å
total_rg	37.59 Å
total_atoms	11818
n_residues	1045
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	113.9 Å
rg_real	39.34 Å
rg_real_error	0.68 Å
i0_real	8.0160e+08
i0_real_error	1.3270e+07
rg_reciprocal	39.51 Å
i0_reciprocal	801700000.0000
total_estimate	0.8826
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.5 Å
skewness	0.085
kurtosis	-0.689
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	59410000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.989; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.513

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone H3.1
formula_weight	15247.8 kDa
mutation	C96S/C110S/K115C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11818

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHACRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H3.1
formula_weight	15304.9 kDa
mutation	C96S/C110S/K115C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHACRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H4
formula_weight	11263.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2A type 1-B/E
formula_weight	14034.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	Histone H2B type 1-J
formula_weight	13804.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 polymer

description	DNA (145-MER)
formula_weight	45007.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTGAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Entity 7 polymer

description	DNA (145-MER)
formula_weight	44505.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTCAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

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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/uz/9uz7/9uz7.fit
pddf	/app/data/pr_computation/uz/9uz7/9uz7.pr.out
profile	/app/data/saxs_computation/uz/9uz7/9uz7.dat

Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)