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9ymd

Structure of AGO2 mature RISC (mat-RISC)

Method: ELECTRON MICROSCOPY D_max: 93.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ymd
deposition_date	2025-10-09
title	Structure of AGO2 mature RISC (mat-RISC)
keywords	Argonaute, mature 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	30.34 Å
rg_electron	29.73 Å
i0	135111000.00
molecular_weight	89840.0 kDa
excluded_volume	111720 Å³
envelope_volume	146600 Å³
shell_volume	40876 Å³
envelope_diameter	98.6 Å
shell_rg	37.34 Å
envelope_rg	29.31 Å
shape_rg	29.71 Å
total_rg	30.50 Å
total_atoms	6299
n_residues	769
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	93.2 Å
rg_real	30.25 Å
rg_real_error	0.47 Å
i0_real	1.3510e+08
i0_real_error	1.7420e+06
rg_reciprocal	30.29 Å
i0_reciprocal	135100000.0000
total_estimate	0.6870
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.263
kurtosis	-0.412
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	28260000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.999; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 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
atom_count	6299

GAMGSMYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	;RNA (5'-R(PUPAPAPAPGPUPGPCPUPAP*G)-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	3.450 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.45 Å
resolution_method	—
num_particles	63912

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

Structure of AGO2 mature RISC (mat-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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)