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9qv5

Asgard Archaeal HHoB nucleosome in the closed conformation

Method: ELECTRON MICROSCOPY D_max: 117.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qv5
deposition_date	2025-04-11
title	Asgard Archaeal HHoB nucleosome in the closed conformation
keywords	Archaea, Asgard, chromatin, nucleosome, 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	39.19 Å
rg_electron	36.96 Å
i0	512006000.00
molecular_weight	127160.0 kDa
excluded_volume	135130 Å³
envelope_volume	227600 Å³
shell_volume	51466 Å³
envelope_diameter	119.6 Å
shell_rg	43.45 Å
envelope_rg	35.60 Å
shape_rg	36.79 Å
total_rg	37.62 Å
total_atoms	8628
n_residues	784
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	117.6 Å
rg_real	38.92 Å
rg_real_error	0.80 Å
i0_real	5.1200e+08
i0_real_error	7.3610e+06
rg_reciprocal	39.10 Å
i0_reciprocal	512100000.0000
total_estimate	0.9110
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	47.0 Å
skewness	0.035
kurtosis	-0.675
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	15870000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Archaeal histone A
formula_weight	7524.6 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	8628

MAGNFANARVEKLIRQAGAQRVSADAVDKMNEILTDWGKNIAKYAVEIARHSGRKTVKENDIKLAAQK

Source

organism	Candidatus Heimdallarchaeota archaeon LC_3
ncbi_taxonomy_id	1841598
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (120-MER) part of a full 147 bp Widom601 DNA
formula_weight	36849.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X

GTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGA

Entity 3 polymer

description	DNA (120-MER) part of a full 147 bp Widom601 DNA
formula_weight	37218.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

TCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCAC

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6. Citations (1)

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resolution	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	117260

fit	/app/data/saxs_computation/qv/9qv5/9qv5.fit
pddf	/app/data/pr_computation/qv/9qv5/9qv5.pr.out
profile	/app/data/saxs_computation/qv/9qv5/9qv5.dat

Asgard Archaeal HHoB nucleosome in the closed conformation

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)