SAXSdb — 9ymc

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1. Structure Basics

entry_id	9ymc
deposition_date	2025-10-09
title	Structure of AGO2 passenger-ejecting RISC (ej-RISC)
keywords	Argonaute, ej-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	30.09 Å
rg_electron	29.66 Å
i0	152882000.00
molecular_weight	93738.0 kDa
excluded_volume	115600 Å³
envelope_volume	150400 Å³
shell_volume	41726 Å³
envelope_diameter	98.8 Å
shell_rg	37.52 Å
envelope_rg	29.44 Å
shape_rg	29.64 Å
total_rg	30.40 Å
total_atoms	6559
n_residues	788
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	93.3 Å
rg_real	30.02 Å
rg_real_error	0.58 Å
i0_real	1.5290e+08
i0_real_error	2.0610e+06
rg_reciprocal	30.05 Å
i0_reciprocal	152900000.0000
total_estimate	0.8963
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.297
kurtosis	-0.376
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	38360000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.840

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

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

Polymer

type	polyribonucleotide
strand_id	C
atom_count	6559

AAGAGACCUGCACUAUAAGCACUUUAAG

Entity 2 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

Entity 3 polymer

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

Polymer

type	polyribonucleotide
strand_id	B

UAAAGUGCUUAUAGUGCAGGUAG

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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	3.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.28 Å
resolution_method	—
num_particles	66044

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

Structure of AGO2 passenger-ejecting RISC (ej-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

Source

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)