SAXSdb — 9yfl

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1. Structure Basics

entry_id	9yfl
deposition_date	2025-09-26
title	insect H/ACA snoRNP class I
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	41.62 Å
rg_electron	40.91 Å
i0	576731000.00
molecular_weight	177100.0 kDa
excluded_volume	213590 Å³
envelope_volume	300630 Å³
shell_volume	61205 Å³
envelope_diameter	155.3 Å
shell_rg	46.38 Å
envelope_rg	40.42 Å
shape_rg	40.89 Å
total_rg	41.23 Å
total_atoms	23832
n_residues	1374
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	143.6 Å
rg_real	41.60 Å
rg_real_error	1.27 Å
i0_real	5.7670e+08
i0_real_error	1.0240e+07
rg_reciprocal	41.62 Å
i0_reciprocal	576700000.0000
total_estimate	0.8744
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.1 Å
skewness	0.323
kurtosis	-0.211
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	37220000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.883

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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 3
formula_weight	7607.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,H
atom_count	23832

MYLRYYLNENGDRQYTLATIDPYGKPTISAHPARFSPEDKYSRHRIIIKKRFGLLLTQQPEPIL

Entity 2 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

MTEVLQPGAEVFSEKKKKKVKESKEGVSLGQFQKLGDFKIEPTESVTKLDTAYWPLLLKNFDRLNVRTNHYTPLPFGHSPLKRPIAEYVKAGFINVDKPSNPSSHEVVSWIKRILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQNAGKEYVAVFSLHSAVENVKKVTQGLEKLRGALFQRPPLISAVKRQLRVRSVYDSKLLDFDKDRNIGVFWVSCEAGSYIRTMCVHLGLMLGVGGQMIELRRVRSGIQGEKEGMVTMHDILDAQWAYENHKDESYLRRVIKPLEGLLVAHKRIFIKDSAVNAVCYGAKVLLPGILRYEDGIEIDQEIVIVTTKGEAVALAIALMTTSTMASCDHGVAAKLKRVIMERDTYPRKWGLGPKASHKKSLISQGKLDKFGKPNENTPSEWLNSYVDYKKKDTNGDAEDDVGRKRTASTANADDPDNSVEVKSEKKKKKKKRDSEAADAVPEDGSGDATMEAETTTEADSSIRKEKKKKKKKDREQERVDE

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
formula_weight	22800.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MSFRGRGGGGGGRGGYGGGGGGGGRGFGGRGGGGGRGGFGGRGGGRGGRGGGGGGFRQQDQGPPESVIPLGHYGWTVQDDLICKVDIEDVPYFNAPIFLENKEQIGKIDEIFGNLRDYFVSVKMGDNFKANSFKDGQQFYIDPAKLLPLKRFLPQPPGAKRGGGRGRGGPRGGRGGGGGFGRGGGGGGRGGGFGRGGGGGRGGFGRGGGGGYGGGGGGFNRGGGGFRGGRGGR

Entity 5 polymer

description	Modeled RNA (101-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	2.90 Å
resolution_method	—
num_particles	760070

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

insect H/ACA snoRNP class I

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)