SAXSdb — 9v43

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1. Structure Basics

entry_id	9v43
deposition_date	2025-05-22
title	Cryo-EM structure of DICER/26S-UG complex in dicing state
keywords	endonuclease, miRNA, dicer, precursor miRNA, HYDROLASE; HYDROLASE
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	32.64 Å
rg_electron	33.49 Å
i0	182636000.00
molecular_weight	98937.0 kDa
excluded_volume	119510 Å³
envelope_volume	149580 Å³
shell_volume	38644 Å³
envelope_diameter	123.0 Å
shell_rg	38.73 Å
envelope_rg	33.56 Å
shape_rg	33.56 Å
total_rg	33.63 Å
total_atoms	6889
n_residues	766
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	113.5 Å
rg_real	32.93 Å
rg_real_error	1.08 Å
i0_real	1.8260e+08
i0_real_error	3.0020e+06
rg_reciprocal	32.81 Å
i0_reciprocal	182600000.0000
total_estimate	0.8328
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.540
kurtosis	-0.290
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	47380000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.885

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA (64-MER)
formula_weight	20545.2 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	6889

UGGAUAUUUCUCGCAGAUCUCAUGUGAAAAAAAAAACACAUGACAUCUGUGAGAAAUAUUCGUA

Entity 2 polymer

description	Endoribonuclease Dicer
formula_weight	217989.0 kDa
ec_number	3.1.26.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGHHHHHHHHHHPFFGLPWQQEAIHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGDFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATDLVVLDRYTSQPCEIVVDCGPFTDRSGLYERLLMELEEALNFINDCNISVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLFTDTFLRKIHALCEEHFSPASLDLKFVTPKVIKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDEDEEIEEKEKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYIMLADTDKIKSFEEDLKTYKAIEKILRNKCSKSVDTGETDIDPVMDDDDVFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRASIVGPPMSCVRLAERVVALICCEKLHKIGELDDHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQCYPKAIPECLRDSYPRPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRLEKPALEFKPTDADSAYCVLPLNVVNDSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRAQTASDAGVGVRSLPADFRYPNLDFGWKKSIDSKSFISISNSSSAENDNYCKHSTIVPENAAHQGANRTSSLENHDQMSVNCRTLLSESPGKLHVEVSADLTAINGLSYNQNLANGSYDLANRDFCQGNQLNYYKQEIPVQPTTSYSIQNLYSYENQPQPSDECTLLSNKYLDGNANKSTSDGSPVMAVMPGTTDTIQVLKGRMDSEQSPSIGYSSRTLGPNPGLILQALTLSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVNWLPPGYVVNQDKSNTDKWEKDEMTKDCMLANGKLDEDYEEEDEEEESLMWRAPKEEADYEDDFLEYDQEHIRFIDNMLMGSGAFVKKISLSPFSTTDSAYEWKMPKKSSLGSMPFSSDFEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTEQCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTDREKALCPTRENFNSQQKNLSVSCAAASVASSRSSVLKDSEYGCLKIPPRCMFDHPDADKTLNHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANVPRSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPQVPNS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

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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	3.340 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.34 Å
resolution_method	—
num_particles	641317

fit	/app/data/saxs_computation/v4/9v43/9v43.fit
pddf	/app/data/pr_computation/v4/9v43/9v43.pr.out
profile	/app/data/saxs_computation/v4/9v43/9v43.dat

Cryo-EM structure of DICER/26S-UG complex in dicing state

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)