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9qv6

Asgard HHoB hypernucleosome in the closed state

Method: ELECTRON MICROSCOPY D_max: 114.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qv6
deposition_date	2025-04-11
title	Asgard HHoB hypernucleosome in the closed state
keywords	archaea, Asgard, chromatin, histone, DNA, 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	40.79 Å
rg_electron	38.26 Å
i0	1207960000.00
molecular_weight	205050.0 kDa
excluded_volume	223100 Å³
envelope_volume	347040 Å³
shell_volume	72296 Å³
envelope_diameter	114.9 Å
shell_rg	47.14 Å
envelope_rg	37.21 Å
shape_rg	38.11 Å
total_rg	38.94 Å
total_atoms	13932
n_residues	1212
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	114.3 Å
rg_real	40.52 Å
rg_real_error	0.53 Å
i0_real	1.2080e+09
i0_real_error	1.7030e+07
rg_reciprocal	40.79 Å
i0_reciprocal	1208000000.0000
total_estimate	0.8770
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.6 Å
skewness	-0.037
kurtosis	-0.697
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	273800000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.479

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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	7796.9 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	13932

SNAMAGNFANARVEKLIRQAGAQRVSADAVDKMNEILTDWGKNIAKYAVEIARHSGRKTVKENDIKLAAQK

Source

organism	Candidatus Heimdallarchaeota archaeon LC_3
ncbi_taxonomy_id	1841598
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (180-MER)
formula_weight	55363.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTG

Entity 3 polymer

description	DNA (180-MER)
formula_weight	55781.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

CAATTGAGCGGCCTCGGCACCGGGATTCTCCAGACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

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6. Citations (1)

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resolution	2.60 Å
resolution_method	—
num_particles	353468

fit	/app/data/saxs_computation/qv/9qv6/9qv6.fit
pddf	/app/data/pr_computation/qv/9qv6/9qv6.pr.out
profile	/app/data/saxs_computation/qv/9qv6/9qv6.dat

Asgard HHoB hypernucleosome in the closed state

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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)