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9zeo

Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1

Method: ELECTRON MICROSCOPY D_max: 117.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zeo
deposition_date	2025-11-30
title	Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1
keywords	chromatin, nucleosome, VHH, antibody, acidic-patch, AP, DE NOVO PROTEIN; DE NOVO 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	41.25 Å
rg_electron	38.81 Å
i0	925084000.00
molecular_weight	188620.0 kDa
excluded_volume	210720 Å³
envelope_volume	322620 Å³
shell_volume	67398 Å³
envelope_diameter	121.0 Å
shell_rg	46.44 Å
envelope_rg	38.05 Å
shape_rg	38.67 Å
total_rg	39.45 Å
total_atoms	12895
n_residues	1174
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	117.5 Å
rg_real	41.02 Å
rg_real_error	0.67 Å
i0_real	9.2510e+08
i0_real_error	1.4570e+07
rg_reciprocal	41.25 Å
i0_reciprocal	925300000.0000
total_estimate	0.8791
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.6 Å
skewness	0.027
kurtosis	-0.690
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	61480000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.991; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.454

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	DNA Tracking Strand
formula_weight	44520.4 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I
atom_count	12895

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source

organism	artificial sequences
ncbi_taxonomy_id	81077
host_organism	Escherichia coli

Entity 2 polymer

description	DNA Lagging Strand
formula_weight	44991.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source

organism	artificial sequences
ncbi_taxonomy_id	81077
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H3.1
formula_weight	11504.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H4
formula_weight	9409.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	Histone H2A type 1-B/E
formula_weight	12167.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 polymer

description	Histone H2B type 1-K
formula_weight	10607.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 7 polymer

description	Single-chain antibody (VHH) 1G1
formula_weight	13460.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

AEVQLVESGGGLVQAGGSLSVSCTASGRTVSSYAMGWFRQAPGKEREFVAGISRRGSRTYYVDSVEGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVRSRGSDYGQIDSYGYWGQGTQVTVS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	136376

fit	/app/data/saxs_computation/ze/9zeo/9zeo.fit
pddf	/app/data/pr_computation/ze/9zeo/9zeo.pr.out
profile	/app/data/saxs_computation/ze/9zeo/9zeo.dat

Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1

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 (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

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)