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9tgn

Cryo-EM structure of Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA

Method: ELECTRON MICROSCOPY D_max: 136.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tgn
deposition_date	2025-12-02
title	Cryo-EM structure of Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
keywords	Z-DNA, monoclonal antibody, left-handed geometry, antibody avidity, 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	38.10 Å
rg_electron	38.25 Å
i0	511169000.00
molecular_weight	170390.0 kDa
excluded_volume	207290 Å³
envelope_volume	284760 Å³
shell_volume	61430 Å³
envelope_diameter	148.8 Å
shell_rg	44.59 Å
envelope_rg	37.85 Å
shape_rg	38.24 Å
total_rg	38.65 Å
total_atoms	11915
n_residues	1440
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	136.1 Å
rg_real	38.01 Å
rg_real_error	1.07 Å
i0_real	5.1120e+08
i0_real_error	8.5560e+06
rg_reciprocal	38.07 Å
i0_reciprocal	511200000.0000
total_estimate	0.8551
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.5 Å
skewness	0.322
kurtosis	-0.198
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	67510000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.718; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.959

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	ZD11-VL
formula_weight	12085.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,C,E,G,I,K
atom_count	11940

DIQMTQTTSSLSASLGDRVTINCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISYLEQEDIATYFCQQGKTLPFTFGAGTKLELKRA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	ZD11-VH
formula_weight	13863.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,J,L

EVQLVETGGGLVQPKGSLKLSCAASGFTFNTNAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRGYVNYYYVMDYWGQGTSVTVSSA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	;DNA (5'-D(CPGPCPGPCPGPCPGPCPGPCPG)-3') ;
formula_weight	3665.4 kDa
src_method	syn
entity_count	4

Polymer

type	polydeoxyribonucleotide
strand_id	M,N,O,P

CGCGCGCGCGCG

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

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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	2.550 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.55 Å
resolution_method	—
num_particles	146988

fit	/app/data/saxs_computation/tg/9tgn/9tgn.fit
pddf	/app/data/pr_computation/tg/9tgn/9tgn.pr.out
profile	/app/data/saxs_computation/tg/9tgn/9tgn.dat

Cryo-EM structure of Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)