SAXSdb — 9ymb

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1. Structure Basics

entry_id	9ymb
deposition_date	2025-10-09
title	Structure of AGO2 wedging RISC (wedg-RISC)
keywords	Argonaute, wedg1-RISC, RNAi, RISC assembly, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING 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	28.76 Å
rg_electron	28.65 Å
i0	113224000.00
molecular_weight	80320.0 kDa
excluded_volume	99012 Å³
envelope_volume	128060 Å³
shell_volume	37579 Å³
envelope_diameter	98.9 Å
shell_rg	35.71 Å
envelope_rg	28.69 Å
shape_rg	28.63 Å
total_rg	29.33 Å
total_atoms	5626
n_residues	674
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	94.2 Å
rg_real	28.79 Å
rg_real_error	0.51 Å
i0_real	1.1320e+08
i0_real_error	1.6160e+06
rg_reciprocal	28.78 Å
i0_reciprocal	113200000.0000
total_estimate	0.8752
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.2 Å
skewness	0.453
kurtosis	-0.137
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0001
highest_alpha	32830000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.882

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	;RNA (5'-R(PUPAPAPAPGPUPGPC)-3') ;
formula_weight	7429.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B
atom_count	5626

UAAAGUGCUUAUAGUGCAGGUAG

Entity 2 polymer

description	;RNA (5'-R(PUPAPAPGPCPAPCPUPUPU)-3') ;
formula_weight	8970.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

AAGAGACCUGCACUAUAAGCACUUUAAG

Entity 3 polymer

description	Protein argonaute-2
formula_weight	97753.6 kDa
ec_number	3.1.26.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GAMGSMYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

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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	3.770 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.77 Å
resolution_method	—
num_particles	64344

fit	/app/data/saxs_computation/ym/9ymb/9ymb.fit
pddf	/app/data/pr_computation/ym/9ymb/9ymb.pr.out
profile	/app/data/saxs_computation/ym/9ymb/9ymb.dat

Structure of AGO2 wedging RISC (wedg-RISC)

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

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)