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9vku

Cryo-EM structure of DRT9 tetramer complex

Method: ELECTRON MICROSCOPY D_max: 195.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vku
deposition_date	2025-06-23
title	Cryo-EM structure of DRT9 tetramer complex
keywords	a protein complex, ANTIVIRAL PROTEIN/RNA, ANTIVIRAL PROTEIN-RNA complex; ANTIVIRAL PROTEIN/RNA
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	58.72 Å
rg_electron	55.84 Å
i0	4917530000.00
molecular_weight	440590.0 kDa
excluded_volume	488950 Å³
envelope_volume	805140 Å³
shell_volume	117850 Å³
envelope_diameter	204.2 Å
shell_rg	60.04 Å
envelope_rg	54.65 Å
shape_rg	55.65 Å
total_rg	56.35 Å
total_atoms	30120
n_residues	2629
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	195.1 Å
rg_real	58.54 Å
rg_real_error	1.48 Å
i0_real	4.9180e+09
i0_real_error	9.4630e+07
rg_reciprocal	58.85 Å
i0_reciprocal	4920000000.0000
total_estimate	0.8842
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.0 Å
skewness	0.217
kurtosis	-0.496
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	262100000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.889

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA-dependent DNA polymerase
formula_weight	58319.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	30120

MKLEQQIQRVILEEAKALIKDYHEYHNRVHLESVRNKKRLGDSAPDKKIHRPNYWSFDKKFDPFYVKSNYKSIARSIANKIENRTYLPNEPFTKDVPKPDGGIRKVSIYQIPDAAISKLFFNRLLAKNRHRFSSFSYAYRNDRNVHFAIQDISVDLKKNERTFLAEFDFSDFFGSISHSFLNEQFNENGFYISPEEKFIIRSFLRERKVGIPQGTSISLFLANLTCWKLDQDLEREGVKFSRYADDTIIWSQEYSKICNAFNIITNFSKSAGIKINPKKSEGISLLTKKGLPSEITSKNNLDFLGYTLSVENVSIKEKSVKKIKKQISYILYRNLIQPLKKTSLAGQTIPANDRDKNFLIAICEIRRYMYGGLSKSQIKDYLSGRSNRLYFKGIMSFYPLVNDVEQLKQLDGWIVSVIYRALKLRCQLLSKWGYNRSHNFPFILDREDIVDKCSKKTIAGRKLFEIPSFLLIHKALQKGLQESGIEKIMNPQSLNYDYE

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	RNA (188-MER)
formula_weight	60361.4 kDa
src_method	man
entity_count	4

Polymer

type	polyribonucleotide
strand_id	E,F,G,H

CAUUCUCUCAUAGGGAUAACGGUGUGGCCUUCUACCUGUUAGAAAUAAUGGGUCUUCAGUUGUAAUUCGUUGCAACUGACGGGGGGGUGGUGUCAAAGCCGUUUCAACCAAGUGGUAACUUACUUUUACUUGGGUUUAUACCGUGGAAAAGCCUGAGUCUAACUCAGGCUUUUUUGUUUAGAGGGCUU

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

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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	3.49 Å
resolution_method	—
num_particles	210060

fit	/app/data/saxs_computation/vk/9vku/9vku.fit
pddf	/app/data/pr_computation/vk/9vku/9vku.pr.out
profile	/app/data/saxs_computation/vk/9vku/9vku.dat

Cryo-EM structure of DRT9 tetramer 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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)