SAXSdb — 9ym9

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1. Structure Basics

entry_id	9ym9
deposition_date	2025-10-09
title	Structure of AGO2 primary RISC (pri-RISC)
keywords	Argonaute, pri-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	26.23 Å
rg_electron	24.84 Å
i0	89028500.00
molecular_weight	64498.0 kDa
excluded_volume	76634 Å³
envelope_volume	96626 Å³
shell_volume	32314 Å³
envelope_diameter	91.0 Å
shell_rg	32.04 Å
envelope_rg	24.99 Å
shape_rg	24.76 Å
total_rg	25.69 Å
total_atoms	4480
n_residues	496
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	87.1 Å
rg_real	26.18 Å
rg_real_error	0.57 Å
i0_real	8.9030e+07
i0_real_error	1.3610e+06
rg_reciprocal	26.20 Å
i0_reciprocal	89030000.0000
total_estimate	0.8812
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	85.7 Å
skewness	0.337
kurtosis	-0.200
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	14300000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	4480

GAMGSMYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

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

Polymer

type	polyribonucleotide
strand_id	B

UAAAGUGCUUAUAGUGCAGGUAG

Entity 3 polymer

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

Polymer

type	polyribonucleotide
strand_id	C

AAGAGACCUGCACUAUAAGCACUUUAAG

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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	3.790 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.79 Å
resolution_method	—
num_particles	203008

fit	/app/data/saxs_computation/ym/9ym9/9ym9.fit
pddf	/app/data/pr_computation/ym/9ym9/9ym9.pr.out
profile	/app/data/saxs_computation/ym/9ym9/9ym9.dat

Structure of AGO2 primary RISC (pri-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

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)