SAXSdb — 9yfn

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1. Structure Basics

entry_id	9yfn
deposition_date	2025-09-26
title	insect H/ACA snoRNP class III
keywords	Pseudouridine synthase, enzyme complex, snoRNA, snoRNP, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	38.18 Å
rg_electron	37.45 Å
i0	397091000.00
molecular_weight	147080.0 kDa
excluded_volume	178030 Å³
envelope_volume	249130 Å³
shell_volume	55225 Å³
envelope_diameter	135.5 Å
shell_rg	43.77 Å
envelope_rg	36.91 Å
shape_rg	37.45 Å
total_rg	37.80 Å
total_atoms	19883
n_residues	1156
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	129.4 Å
rg_real	38.04 Å
rg_real_error	1.29 Å
i0_real	3.9710e+08
i0_real_error	7.2140e+06
rg_reciprocal	38.13 Å
i0_reciprocal	397100000.0000
total_estimate	0.6101
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	47.4 Å
skewness	0.210
kurtosis	-0.376
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	24670000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	H/ACA ribonucleoprotein complex subunit 4-like
formula_weight	57643.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	19883

MTEVLQPGAEVFSEKKKKKVKESKEGVSLGQFQKLGDFKIEPTESVTKLDTAYWPLLLKNFDRLNVRTNHYTPLPFGHSPLKRPIAEYVKAGFINVDKPSNPSSHEVVSWIKRILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQNAGKEYVAVFSLHSAVENVKKVTQGLEKLRGALFQRPPLISAVKRQLRVRSVYDSKLLDFDKDRNIGVFWVSCEAGSYIRTMCVHLGLMLGVGGQMIELRRVRSGIQGEKEGMVTMHDILDAQWAYENHKDESYLRRVIKPLEGLLVAHKRIFIKDSAVNAVCYGAKVLLPGILRYEDGIEIDQEIVIVTTKGEAVALAIALMTTSTMASCDHGVAAKLKRVIMERDTYPRKWGLGPKASHKKSLISQGKLDKFGKPNENTPSEWLNSYVDYKKKDTNGDAEDDVGRKRTASTANADDPDNSVEVKSEKKKKKKKRDSEAADAVPEDGSGDATMEAETTTEADSSIRKEKKKKKKKDREQERVDE

Entity 2 polymer

description	H/ACA ribonucleoprotein complex subunit
formula_weight	22800.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MSFRGRGGGGGGRGGYGGGGGGGGRGFGGRGGGGGRGGFGGRGGGRGGRGGGGGGFRQQDQGPPESVIPLGHYGWTVQDDLICKVDIEDVPYFNAPIFLENKEQIGKIDEIFGNLRDYFVSVKMGDNFKANSFKDGQQFYIDPAKLLPLKRFLPQPPGAKRGGGRGRGGPRGGRGGGGGFGRGGGGGGRGGGFGRGGGGGRGGFGRGGGGGYGGGGGGFNRGGGGFRGGRGGR

Entity 3 polymer

description	H/ACA ribonucleoprotein complex subunit 3
formula_weight	7607.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,H

MYLRYYLNENGDRQYTLATIDPYGKPTISAHPARFSPEDKYSRHRIIIKKRFGLLLTQQPEPIL

Entity 4 polymer

description	H/ACA ribonucleoprotein complex subunit 2-like protein
formula_weight	17704.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MGKIKQEPVEQEDQADVSVKNEPQSYDEKVDHCSVIAKPMAPKKLSKKIYKLIKKSTSHKNYIRNGLKIVQKQLRLGEKGIVFFAGDISPIEIMCHLPAVCEEKDIPYCYTPSRKDIGAAMGTMRGCVMVLVKEHDDYKDLFDEVRGEIKLLGHPI

Entity 5 polymer

description	RNA (76-MER)
formula_weight	24486.7 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	J

CCUGCGGCGUGCACGUCCCAACUGGGACGUGCACCGGCCGCAGGAACAGCAACGGAGCGAGUACUCGCUCACACAU

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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	triclinic

resolution	3.14 Å
resolution_method	—
num_particles	134862

fit	/app/data/saxs_computation/yf/9yfn/9yfn.fit
pddf	/app/data/pr_computation/yf/9yfn/9yfn.pr.out
profile	/app/data/saxs_computation/yf/9yfn/9yfn.dat

insect H/ACA snoRNP class III

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)