← Back to search

9ux9

local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state

Method: ELECTRON MICROSCOPY D_max: 147.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ux9
deposition_date	2025-05-13
title	local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state
keywords	Chromatin remodeling, SWI/SNF, Epigenetics, GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/DNA
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	44.54 Å
rg_electron	43.64 Å
i0	1037430000.00
molecular_weight	217420.0 kDa
excluded_volume	252220 Å³
envelope_volume	383350 Å³
shell_volume	73242 Å³
envelope_diameter	149.0 Å
shell_rg	48.56 Å
envelope_rg	42.90 Å
shape_rg	43.58 Å
total_rg	43.98 Å
total_atoms	14988
n_residues	1496
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	147.1 Å
rg_real	44.49 Å
rg_real_error	1.22 Å
i0_real	1.0370e+09
i0_real_error	1.9380e+07
rg_reciprocal	44.54 Å
i0_reciprocal	1037000000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.4 Å
skewness	0.304
kurtosis	-0.397
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	101400000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.775

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (10)

Entity 1 polymer

description	Histone H3
formula_weight	15303.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	14988

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	14163.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

NASGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source

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

Entity 4 polymer

description	Histone H2B
formula_weight	13524.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

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

Entity 5 polymer

description	DNA (167-MER)
formula_weight	51271.6 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCTAGAGCGGCCGCCACCGC

Source

organism	artificial sequences
ncbi_taxonomy_id	81077
host_organism	synthetic construct

Entity 6 polymer

description	DNA (167-MER)
formula_weight	51841.0 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

GCGGTGGCGGCCGCTCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Source

organism	artificial sequences
ncbi_taxonomy_id	81077
host_organism	synthetic construct

Entity 7 polymer

description	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
formula_weight	184934.8 kDa
ec_number	3.6.4.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MASTPDPPLGGTPRPGPSPGPGPSPGAMLGPSPGPSPGSAHSMMGPSPGPPSAGHPIPTQGPGGYPQDNMHQMHKPMESMHEKGMSDDPRYNQMKGMGMRSGGHAGMGPPPSPMDQHSQGYPSPLGGSEHASSPVPASGPSSGPQMSSGPGGAPLDGADPQALGQQNRGPTPFNQNQLHQLRAQIMAYKMLARGQPLPDHLQMAVQGKRPMPGMQQQMPTLPPPSVSATGPGPGPGPGPGPGPGPAPPNYSRPHGMGGPNMPPPGPSGVPPGMPGQPPGGPPKPWPEGPMANAAAPTSTPQKLIPPQPTGRPSPAPPAVPPAASPVMPPQTQSPGQPAQPAPMVPLHQKQSRITPIQKPRGLDPVEILQEREYRLQARIAHRIQELENLPGSLAGDLRTKATIELKALRLLNFQRQLRQEVVVCMRRDTALETALNAKAYKRSKRQSLREARITEKLEKQQKIEQERKRRQKHQEYLNSILQHAKDFKEYHRSVTGKIQKLTKAVATYHANTEREQKKENERIEKERMRRLMAEDEEGYRKLIDQKKDKRLAYLLQQTDEYVANLTELVPQHKAAQVAKEKKKKKKKKKAENAEGQTPAIGPDGEPLDETSQMSDLPVKVIHVESGKILTGTDAPKAGQLEAWLEMNPGYEVAPRSDSEESGSEEEEEEEEEEQPQAAQPPTLPVEEKKKIPDPDSDDVSEVDARHIIENAKQDVDDEYGVSQALARGLQSYYAVAHAVTERVDKQSALMVNGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNWAYEFDKWAPSVVKVSYKGSPAARRAFVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLNTHYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNAPFAMTGEKVDLNEEETILIIRRLHKVLRPFLLRRLKKEVEAQLPEKVEYVIKCDMSALQRVLYRHMQAKGVLLTDGSEKDKKGKGGTKTLMNTIMQLRKICNHPYMFQHIEESFSEHLGFTGGIVQGLDLYRASGKFELLDRILPKLRATNHKVLLFCQMTSLMTIMEDYFAYRGFKYLRLDGTTKAEDRGMLLKTFNEPGSEYFIFLLSTRAGGLGLNLQSADTVIIFDSDWNPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEQDESRHCSTGSGSASFAHTAPPPAGVNPDLEEPPLKEEDEVPDDETVNQMIARHEEEFDLFMRMDLDRRREEARNPKRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKMFGRGSRHRKEVDYSDSLTEKQWLKAIEEGTLEEIEEEVRQKKSSRKRKRDSDAGSSTPTTSTRSRDKDDESKKQKKRGRPPAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEGEESEEEEEGEEEGSESESRSVKVKIKLGRKEKAQDRLKGGRRRPSRGSRAKPVVSDDDSEEEQEEDRSGSGSEED

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mammalia

Entity 8 non-polymer

description	BERYLLIUM TRIFLUORIDE ION
formula_weight	66.0 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

▶

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	3.050 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.05 Å
resolution_method	—
num_particles	72416

fit	/app/data/saxs_computation/ux/9ux9/9ux9.fit
pddf	/app/data/pr_computation/ux/9ux9/9ux9.pr.out
profile	/app/data/saxs_computation/ux/9ux9/9ux9.dat

local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state

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

Refinement

EM 3D

5. Entities & Polymer Info (10)

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 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)