SAXSdb — 9qaj

▼

1. Structure Basics

entry_id	9qaj
deposition_date	2025-02-28
last_revision	2025-04-23
title	Structure of the nucleosome-bound human BCL7A
keywords	Nucleosome, acidic patch, BCL7A, arginine anchor, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	40.16 Å
rg_electron	37.50 Å
i0	850741000.00
molecular_weight	177880.0 kDa
excluded_volume	197250 Å³
envelope_volume	293420 Å³
shell_volume	63574 Å³
envelope_diameter	116.7 Å
shell_rg	44.99 Å
envelope_rg	36.81 Å
shape_rg	37.34 Å
total_rg	38.18 Å
total_atoms	12144
n_residues	1086
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

▼

3. P(r) Analysis (GNOM)

dmax	117.6 Å
rg_real	39.97 Å
rg_real_error	0.84 Å
i0_real	8.5070e+08
i0_real_error	1.4120e+07
rg_reciprocal	40.16 Å
i0_reciprocal	850900000.0000
total_estimate	0.8961
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.2 Å
skewness	0.068
kurtosis	-0.678
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	52220000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.728

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 polymer

description	Histone H3.2
formula_weight	15303.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	12144

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	11263.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A
formula_weight	12941.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B 1.1
formula_weight	13848.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 5 polymer

description	601 DNA
formula_weight	44991.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 polymer

description	601 DNA
formula_weight	44520.4 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 7 polymer

description	Isoform 2 of B-cell CLL/lymphoma 7 protein family member A
formula_weight	1567.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,M

MSGRSVRAETRSRA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 8 polymer

description	Isoform 2 of B-cell CLL/lymphoma 7 protein family member A
formula_weight	1906.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,N

KDDIKRVMAAIEKVRK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

▶

6. Citations (1)

▶

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	2.95 Å
resolution_method	—
num_particles	563788

fit	/app/data/saxs_computation/qa/9qaj/9qaj.fit
pddf	/app/data/pr_computation/qa/9qaj/9qaj.pr.out
profile	/app/data/saxs_computation/qa/9qaj/9qaj.dat

Structure of the nucleosome-bound human BCL7A

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 (8)

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

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)