SAXSdb — 9vma

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1. Structure Basics

entry_id	9vma
deposition_date	2025-06-27
title	Cryo-EM structure of substrate-bound DRT9 hexamer complex
keywords	complex, ANTIVIRAL PROTEIN/RNA/DNA, ANTIVIRAL PROTEIN-RNA-DNA complex; ANTIVIRAL PROTEIN/RNA/DNA
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	62.50 Å
rg_electron	59.27 Å
i0	11259300000.00
molecular_weight	667340.0 kDa
excluded_volume	739050 Å³
envelope_volume	1213500 Å³
shell_volume	161780 Å³
envelope_diameter	205.8 Å
shell_rg	67.88 Å
envelope_rg	58.14 Å
shape_rg	59.08 Å
total_rg	59.83 Å
total_atoms	45606
n_residues	3963
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	199.8 Å
rg_real	62.01 Å
rg_real_error	1.23 Å
i0_real	1.1260e+10
i0_real_error	2.1910e+08
rg_reciprocal	62.89 Å
i0_reciprocal	11280000000.0000
total_estimate	0.8786
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	79.9 Å
skewness	0.072
kurtosis	-0.528
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0005
highest_alpha	881600000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	RNA-dependent DNA polymerase
formula_weight	58319.0 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	45606

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	6

Polymer

type	polyribonucleotide
strand_id	G,H,I,J,K,L

CAUUCUCUCAUAGGGAUAACGGUGUGGCCUUCUACCUGUUAGAAAUAAUGGGUCUUCAGUUGUAAUUCGUUGCAACUGACGGGGGGGUGGUGUCAAAGCCGUUUCAACCAAGUGGUAACUUACUUUUACUUGGGUUUAUACCGUGGAAAAGCCUGAGUCUAACUCAGGCUUUUUUGUUUAGAGGGCUU

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 polymer

description	;DNA (5'-D(PAPAPAPA)-3') ;
formula_weight	1207.9 kDa
src_method	man
entity_count	6

Polymer

type	polydeoxyribonucleotide
strand_id	M,N,O,P,Q,R

AAAA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 non-polymer

description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
formula_weight	491.2 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	12

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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	3.46 Å
resolution_method	—
num_particles	40373

fit	/app/data/saxs_computation/vm/9vma/9vma.fit
pddf	/app/data/pr_computation/vm/9vma/9vma.pr.out
profile	/app/data/saxs_computation/vm/9vma/9vma.dat

Cryo-EM structure of substrate-bound DRT9 hexamer 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)