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9v9g

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

Method: ELECTRON MICROSCOPY D_max: 95.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9g
deposition_date	2025-05-30
title	Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA in monomeric state.
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	30.12 Å
rg_electron	29.76 Å
i0	173987000.00
molecular_weight	96567.0 kDa
excluded_volume	117480 Å³
envelope_volume	155660 Å³
shell_volume	42886 Å³
envelope_diameter	99.8 Å
shell_rg	37.71 Å
envelope_rg	29.63 Å
shape_rg	29.78 Å
total_rg	30.37 Å
total_atoms	6766
n_residues	794
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	95.7 Å
rg_real	30.02 Å
rg_real_error	0.47 Å
i0_real	1.7400e+08
i0_real_error	2.4830e+06
rg_reciprocal	30.06 Å
i0_reciprocal	174000000.0000
total_estimate	0.8918
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.1 Å
skewness	0.283
kurtosis	-0.326
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0001
highest_alpha	36710000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	VbAgo
formula_weight	88463.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6784

MSEKQLGATLFPITGLPAQAFRLRVLRVRETIPMDTQTPVRLNRWATQLWKELKQAVVPTGRFEWPAFLTPDVESLTVGRVLTVQDVPDREYSIEVIGETVEVNPASASSEELQLAGEMIKRAISDAFGRNSDKYWRKHWNLYFRLEPENLQDRRDRVFAYRGLKFSVVFLGDKPWLAADILTTYHGQHALSEYSSEQRQRELHFHVSERIEADDRAMFLRDNGKIKIPCRFVGSTGKTVTQYTFPINGGQKNVREYYEQRYGIRVPENDEAVFVRDREGCDSWPVPASRLFPLFTTEYDEVRNCSVVPQMPPDERVETIRAFLNDLRDVSFAGSTLAIGHSHFQTAERSVFPAPALEFGNGQTLTVDASLPIEEGYNRYRQGKMTMLYEHGPFSSQSLPDLVLLYPDNLDRNAREKLRQRLGEEIKELCGVAPRIARQISYPLGKQPHAGAGLLAAADELVRNNDGTFLPVIVLADALREHIYDLLKRRLSSLASQCVRERTVARVARDEQAVGGSRLRNLALGILTAAGLQPWVLAKPLHYDFYMGVDLLANQVIYVFVCGKGGRNVWVQRGDQLRRRGITEKIDRVQLADQFKTGVREAKRLGVPLNSLVVHRDGRWWSNEDLAITEAVAELQGDGTLSKDCQVGVVEVRKSHLPVRLFSVLNATKGSLENPMPGSHLILNNTEAILTPTGQPGRWDKQGRTAGTLLLRITRNPNGSPLDIRKIAEDAYGLTHLNWNAPDIEISLPVTIRWSDERLREIVTNPSATDDTEVEPQETCIV

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	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TGAGGTAGTAGGTTGTAT

Entity 3 polymer

description	;RNA (5'-R(UPAPUPAPCPAPAPCPCPUPAPCPUPAPCPCPUPCP*A)-3') ;
formula_weight	5926.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

UAUACAACCUACUACCUCA

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (1)

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resolution	2.890 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.89 Å
resolution_method	—
num_particles	132500

fit	/app/data/saxs_computation/v9/9v9g/9v9g.fit
pddf	/app/data/pr_computation/v9/9v9g/9v9g.pr.out
profile	/app/data/saxs_computation/v9/9v9g/9v9g.dat

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

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)