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9v7s

Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA

Method: ELECTRON MICROSCOPY D_max: 114.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v7s
deposition_date	2025-05-28
title	Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA
keywords	Mesophilic prokaryotic Argonaute, RNA BINDING PROTEIN/DNA/RNA, RNA BINDING PROTEIN-DNA-RNA complex; RNA BINDING PROTEIN/DNA/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	37.39 Å
rg_electron	37.08 Å
i0	643933000.00
molecular_weight	191350.0 kDa
excluded_volume	233150 Å³
envelope_volume	322680 Å³
shell_volume	68914 Å³
envelope_diameter	119.7 Å
shell_rg	46.13 Å
envelope_rg	36.23 Å
shape_rg	37.11 Å
total_rg	37.52 Å
total_atoms	13413
n_residues	1577
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	114.2 Å
rg_real	37.12 Å
rg_real_error	0.48 Å
i0_real	6.4390e+08
i0_real_error	1.0400e+07
rg_reciprocal	37.29 Å
i0_reciprocal	644000000.0000
total_estimate	0.9024
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	46.2 Å
skewness	0.097
kurtosis	-0.572
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0001
highest_alpha	135100000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	VbAgo-DM
formula_weight	88375.3 kDa
mutation	D550A/D617A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,a
atom_count	13421

MSEKQLGATLFPITGLPAQAFRLRVLRVRETIPMDTQTPVRLNRWATQLWKELKQAVVPTGRFEWPAFLTPDVESLTVGRVLTVQDVPDREYSIEVIGETVEVNPASASSEELQLAGEMIKRAISDAFGRNSDKYWRKHWNLYFRLEPENLQDRRDRVFAYRGLKFSVVFLGDKPWLAADILTTYHGQHALSEYSSEQRQRELHFHVSERIEADDRAMFLRDNGKIKIPCRFVGSTGKTVTQYTFPINGGQKNVREYYEQRYGIRVPENDEAVFVRDREGCDSWPVPASRLFPLFTTEYDEVRNCSVVPQMPPDERVETIRAFLNDLRDVSFAGSTLAIGHSHFQTAERSVFPAPALEFGNGQTLTVDASLPIEEGYNRYRQGKMTMLYEHGPFSSQSLPDLVLLYPDNLDRNAREKLRQRLGEEIKELCGVAPRIARQISYPLGKQPHAGAGLLAAADELVRNNDGTFLPVIVLADALREHIYDLLKRRLSSLASQCVRERTVARVARDEQAVGGSRLRNLALGILTAAGLQPWVLAKPLHYDFYMGVALLANQVIYVFVCGKGGRNVWVQRGDQLRRRGITEKIDRVQLADQFKTGVREAKRLGVPLNSLVVHRAGRWWSNEDLAITEAVAELQGDGTLSKDCQVGVVEVRKSHLPVRLFSVLNATKGSLENPMPGSHLILNNTEAILTPTGQPGRWDKQGRTAGTLLLRITRNPNGSPLDIRKIAEDAYGLTHLNWNAPDIEISLPVTIRWSDERLREIVTNPSATDDTEVEPQETCIV

Source

organism	Verrucomicrobiota bacterium
ncbi_taxonomy_id	2026799
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PTPGPAPGPGPTPAPGPTPAPGPGPTPTPGPTPAPT)-3') ;
formula_weight	5641.7 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	B,b

TGAGGTAGTAGGTTGTAT

Entity 3 polymer

description	;RNA (5'-R(UPAPUPAPCPAPAPCPCPUPAPCPUPAPCPCPUPCP*A)-3') ;
formula_weight	5926.6 kDa
src_method	syn
entity_count	2

Polymer

type	polyribonucleotide
strand_id	C,c

UAUACAACCUACUACCUCA

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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resolution	2.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.50 Å
resolution_method	—
num_particles	1016135

fit	/app/data/saxs_computation/v7/9v7s/9v7s.fit
pddf	/app/data/pr_computation/v7/9v7s/9v7s.pr.out
profile	/app/data/saxs_computation/v7/9v7s/9v7s.dat

Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)