SAXSdb — 9yfo

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1. Structure Basics

entry_id	9yfo
deposition_date	2025-09-26
title	insect H/ACA snoRNP class IV
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	39.84 Å
rg_electron	38.48 Å
i0	501388000.00
molecular_weight	163410.0 kDa
excluded_volume	196520 Å³
envelope_volume	272180 Å³
shell_volume	57963 Å³
envelope_diameter	131.3 Å
shell_rg	45.42 Å
envelope_rg	37.72 Å
shape_rg	38.42 Å
total_rg	39.02 Å
total_atoms	21932
n_residues	1264
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	128.5 Å
rg_real	39.65 Å
rg_real_error	0.84 Å
i0_real	5.0140e+08
i0_real_error	7.7140e+06
rg_reciprocal	39.77 Å
i0_reciprocal	501400000.0000
total_estimate	0.9004
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.2 Å
skewness	0.151
kurtosis	-0.544
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	31920000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.929

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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	21932

MTEVLQPGAEVFSEKKKKKVKESKEGVSLGQFQKLGDFKIEPTESVTKLDTAYWPLLLKNFDRLNVRTNHYTPLPFGHSPLKRPIAEYVKAGFINVDKPSNPSSHEVVSWIKRILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQNAGKEYVAVFSLHSAVENVKKVTQGLEKLRGALFQRPPLISAVKRQLRVRSVYDSKLLDFDKDRNIGVFWVSCEAGSYIRTMCVHLGLMLGVGGQMIELRRVRSGIQGEKEGMVTMHDILDAQWAYENHKDESYLRRVIKPLEGLLVAHKRIFIKDSAVNAVCYGAKVLLPGILRYEDGIEIDQEIVIVTTKGEAVALAIALMTTSTMASCDHGVAAKLKRVIMERDTYPRKWGLGPKASHKKSLISQGKLDKFGKPNENTPSEWLNSYVDYKKKDTNGDAEDDVGRKRTASTANADDPDNSVEVKSEKKKKKKKRDSEAADAVPEDGSGDATMEAETTTEADSSIRKEKKKKKKKDREQERVDE

Entity 2 polymer

description	H/ACA ribonucleoprotein complex subunit
formula_weight	22800.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSFRGRGGGGGGRGGYGGGGGGGGRGFGGRGGGGGRGGFGGRGGGRGGRGGGGGGFRQQDQGPPESVIPLGHYGWTVQDDLICKVDIEDVPYFNAPIFLENKEQIGKIDEIFGNLRDYFVSVKMGDNFKANSFKDGQQFYIDPAKLLPLKRFLPQPPGAKRGGGRGRGGPRGGRGGGGGFGRGGGGGGRGGGFGRGGGGGRGGFGRGGGGGYGGGGGGFNRGGGGFRGGRGGR

Entity 3 polymer

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

Polymer

type	polypeptide(L)
strand_id	C,G

MGKIKQEPVEQEDQADVSVKNEPQSYDEKVDHCSVIAKPMAPKKLSKKIYKLIKKSTSHKNYIRNGLKIVQKQLRLGEKGIVFFAGDISPIEIMCHLPAVCEEKDIPYCYTPSRKDIGAAMGTMRGCVMVLVKEHDDYKDLFDEVRGEIKLLGHPI

Entity 4 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 5 polymer

description	RNA (97-MER)
formula_weight	44371.9 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	I

CCUGCGGCAAAAAAAGUGCACGUCCCAAAACUGGGACGUGCACCAAAAAAAAGGCCGCAGGAACAGCAACGGAGCGAGUAAAAAAAAUGCACGUCCCAAAACUGGGACGUGCACAAAAAAAAAACUCGCUCACACAU

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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	3.23 Å
resolution_method	—
num_particles	74734

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

insect H/ACA snoRNP class IV

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)