SAXSdb — 9r1d

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1. Structure Basics

entry_id	9r1d
deposition_date	2025-04-26
title	Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei
keywords	nucleosome, histone, nucleus, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	38.23 Å
rg_electron	35.42 Å
i0	564832000.00
molecular_weight	144860.0 kDa
excluded_volume	161080 Å³
envelope_volume	236310 Å³
shell_volume	54925 Å³
envelope_diameter	113.5 Å
shell_rg	42.68 Å
envelope_rg	34.85 Å
shape_rg	35.26 Å
total_rg	36.15 Å
total_atoms	9880
n_residues	889
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	109.9 Å
rg_real	37.97 Å
rg_real_error	0.61 Å
i0_real	5.6480e+08
i0_real_error	9.0990e+06
rg_reciprocal	38.13 Å
i0_reciprocal	564900000.0000
total_estimate	0.8834
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.6 Å
skewness	0.063
kurtosis	-0.623
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	17000000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.987; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.529

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Histone H3 variant
formula_weight	15920.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	9880

AQMKKITPRPVRPKSVASRPIQSVARAPVKKVENTPPQKRHHRWRPGTVALREIRRLQSSTDFLIQRAPFRRFLREVVSNLKDSYRMSAACVDAIQEATETYITSVFMDANLCTLHANRVTLFPKDIQLALKLRGERN

Source

organism	Trypanosoma brucei brucei TREU927
ncbi_taxonomy_id	185431
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Histone H4
formula_weight	11150.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

AKGKRVGESKGAQKRQKKVLRDNVRGITRGSIRRLARRAGVKRISGVIYDEVRGVLKTFVESIVRDAGAYTEYSRKKTVTAAHVVFALRKRGKVLYGYD

Source

organism	Trypanosoma brucei brucei TREU927
ncbi_taxonomy_id	185431
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Histone H2A
formula_weight	14108.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

ATPKQAVKKASKGGSSRSVKAGLIFPVGRVGTLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQTKKTKRLTPRTVTLAVRHDDDLGALLRNVTMSRGGVMPSLNKALAKKQKSGKHAKATPSV

Source

organism	Trypanosoma brucei brucei TREU927
ncbi_taxonomy_id	185431
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Histone H2B
formula_weight	12464.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

ATPKSTPAKTRKEAKKTRRQRKRTWNVYVSRSLRSINSQMSMTSRTMKIVNSFVNDLFERIAAEAATIVRVNRKRTLGARELQTAVRLVLPADLAKHAMAEGTKAVSHASS

Source

organism	Trypanosoma brucei brucei TREU927
ncbi_taxonomy_id	185431
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	Widom 601 145 bp DNA (115-mer ordered and built)
formula_weight	44991.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 6 polymer

description	Widom 601 145 bp DNA (115-mer ordered and built)
formula_weight	44520.4 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

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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	3.21 Å
resolution_method	—
num_particles	362400

fit	/app/data/saxs_computation/r1/9r1d/9r1d.fit
pddf	/app/data/pr_computation/r1/9r1d/9r1d.pr.out
profile	/app/data/saxs_computation/r1/9r1d/9r1d.dat

Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei

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 (6)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)