SAXSdb — 9wc0

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1. Structure Basics

entry_id	9wc0
deposition_date	2025-08-15
title	The structure of NCP-RA module of ncBAF-nucleosome complex
keywords	Chromatin remodeling complex, GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/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	41.51 Å
rg_electron	38.72 Å
i0	905796000.00
molecular_weight	182340.0 kDa
excluded_volume	201270 Å³
envelope_volume	308980 Å³
shell_volume	64833 Å³
envelope_diameter	136.0 Å
shell_rg	46.06 Å
envelope_rg	38.37 Å
shape_rg	38.54 Å
total_rg	39.42 Å
total_atoms	12431
n_residues	1085
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	128.7 Å
rg_real	41.34 Å
rg_real_error	0.80 Å
i0_real	9.0580e+08
i0_real_error	1.4190e+07
rg_reciprocal	41.51 Å
i0_reciprocal	906000000.0000
total_estimate	0.8987
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	125.3 Å
skewness	0.120
kurtosis	-0.601
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	65710000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.870

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone H4
formula_weight	11263.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F
atom_count	12431

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

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

Entity 2 polymer

description	Histone H2A
formula_weight	13978.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source

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

Entity 3 polymer

description	Histone H2B 1.1
formula_weight	13834.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

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

Entity 4 polymer

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

Polymer

type	polypeptide(L)
strand_id	E,K

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

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

Entity 5 polymer

description	DNA (207-MER)
formula_weight	63553.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGAATCACCCCACGAAGTACTAGAGGATCATAATCAGCCATAC

Entity 6 polymer

description	DNA (207-MER)
formula_weight	64272.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

GTATGGCTGATTATGATCCTCTAGTACTTCGTGGGGTGATTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTATAGGGTCC

Entity 7 polymer

description	B-cell CLL/lymphoma 7 protein family member A
formula_weight	22842.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

MSGRSVRAETRSRAKDDIKRVMAAIEKVRKWEKKWVTVGDTSLRIYKWVPVTEPKVDDKNKNKKKGKDEKCGSEVTTPENSSSPGMMDMHDDNSNQSSIADASPIKQENSSNSSPAPEPNSAVPSDGTEAKVDEAQADGKEHPGAEDASDEQNSQSSMEHSMNSSEKVDRQPSGDSGLAAETSAISQDLEGVPPSKKMKLEASQQNSEEM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	2.40 Å
resolution_method	—
num_particles	635115

fit	/app/data/saxs_computation/wc/9wc0/9wc0.fit
pddf	/app/data/pr_computation/wc/9wc0/9wc0.pr.out
profile	/app/data/saxs_computation/wc/9wc0/9wc0.dat

The structure of NCP-RA module of ncBAF-nucleosome complex

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 (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

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)