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9v9i

The transition-state structure of the Argonaute protein from a Verrucomicrobia bacterium in complex with guide DNA and target RNA.

Method: ELECTRON MICROSCOPY D_max: 94.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9i
deposition_date	2025-05-30
title	The transition-state structure of the Argonaute protein from a 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	30.09 Å
rg_electron	29.71 Å
i0	170500000.00
molecular_weight	95711.0 kDa
excluded_volume	116510 Å³
envelope_volume	155120 Å³
shell_volume	42824 Å³
envelope_diameter	99.1 Å
shell_rg	37.71 Å
envelope_rg	29.56 Å
shape_rg	29.73 Å
total_rg	30.34 Å
total_atoms	6708
n_residues	789
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	94.9 Å
rg_real	29.99 Å
rg_real_error	0.44 Å
i0_real	1.7050e+08
i0_real_error	2.4920e+06
rg_reciprocal	30.04 Å
i0_reciprocal	170500000.0000
total_estimate	0.8924
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.278
kurtosis	-0.330
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	35980000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.910

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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	6716

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	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	2.930 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.93 Å
resolution_method	—
num_particles	114582

fit	/app/data/saxs_computation/v9/9v9i/9v9i.fit
pddf	/app/data/pr_computation/v9/9v9i/9v9i.pr.out
profile	/app/data/saxs_computation/v9/9v9i/9v9i.dat

The transition-state structure of the Argonaute protein from a 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)