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9vzx

Cryo-EM structure of TasH-tigRNA-gap dsDNA complex

Method: ELECTRON MICROSCOPY D_max: 93.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vzx
deposition_date	2025-07-23
title	Cryo-EM structure of TasH-tigRNA-gap dsDNA complex
keywords	protein complex, ANTIVIRAL PROTEIN; ANTIVIRAL 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	28.26 Å
rg_electron	28.63 Å
i0	133434000.00
molecular_weight	75598.0 kDa
excluded_volume	87794 Å³
envelope_volume	111580 Å³
shell_volume	33320 Å³
envelope_diameter	96.9 Å
shell_rg	35.23 Å
envelope_rg	28.34 Å
shape_rg	28.70 Å
total_rg	28.97 Å
total_atoms	5222
n_residues	549
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	93.3 Å
rg_real	28.34 Å
rg_real_error	0.70 Å
i0_real	1.3340e+08
i0_real_error	1.9340e+06
rg_reciprocal	28.32 Å
i0_reciprocal	133400000.0000
total_estimate	0.8780
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.7 Å
skewness	0.443
kurtosis	-0.288
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	17070000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.937

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HNH nuclease domain-containing protein
formula_weight	40031.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5222

MNKQVLKEQASHCEITGAPLAGLPELVDVDRITERFQGGTYTPDNTRVLTPRAHMERHGILRERDQWLEELKAMMDDRAQTMKVVMKMNNQLLAYQRQTDHARQSTEQFLQDTLDASNKRLAQIDREVTKHIKHAKDPLAQAAMGVPGVGPITVAGLQTYVDLEKAKSASALWAYIGIDKPSHDRYTKGEAGGGNKTLRTMVWNMANSMIKNRKCPYRTVYEQTKERLAVSEKVTKSRNTQGQLIECAWKDTKPSHRHGAALRAVMKHFLADYWFVGRELAGLDTRPLYVQEKLGHTGIVQPQERGWEWGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEKNLYFQSGSHHHHHH

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 2 polymer

description	RNA (36-MER)
formula_weight	11948.2 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

AGUCAUUCCGUUAAAGACAACCACGGAGACGAAGCGA

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 3 polymer

description	DNA (38-MER)
formula_weight	11778.6 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

AAATTGATGACGGAGACGATTAACGGAATCGAAACCAC

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 4 polymer

description	DNA (38-MER)
formula_weight	11608.4 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

GTGGTTTCGATTCCGTTAATCGTCTCCGTCATCAATTT

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
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	2.78 Å
resolution_method	—
num_particles	65896

fit	/app/data/saxs_computation/vz/9vzx/9vzx.fit
pddf	/app/data/pr_computation/vz/9vzx/9vzx.pr.out
profile	/app/data/saxs_computation/vz/9vzx/9vzx.dat

Cryo-EM structure of TasH-tigRNA-gap dsDNA complex

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)