SAXSdb — 9yfo

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1. Protein Identity and Related Structures Protein Identity & Related Structures

H/ACA ribonucleoprotein complex subunit 4-like

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 7 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 1–514 Chain D； UniProt 1–514	Not recorded	H/ACA ribonucleoprotein complex subunit × 1 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） RNA (97-MER) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.23 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YFO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YFL insect H/ACA snoRNP class I Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain A 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9YFM insect H/ACA snoRNP class II composite Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain A 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9YFN insect H/ACA snoRNP class III Deposited 2025-09-26	Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain A 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7E5VBG0_TRINI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–514； UniProt 1–514 Author chain D； PDBConstruct 1–514； UniProt 1–514

H/ACA ribonucleoprotein complex subunit

OrganismNot specified

UniProt A0A7E5WAP8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 7 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts	Chain B； UniProt 1–233	Not recorded	H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） RNA (97-MER) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.23 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YFO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YFL insect H/ACA snoRNP class I Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain B 1–233（233 aa） Chain E 1–233（233 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9YFM insect H/ACA snoRNP class II composite Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain B 1–233（233 aa） Chain E 1–233（233 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9YFN insect H/ACA snoRNP class III Deposited 2025-09-26	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain B 1–233（233 aa） Chain E 1–233（233 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7E5WAP8_TRINI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–233； UniProt 1–233

H/ACA ribonucleoprotein complex subunit 2-like protein

OrganismNot specified

UniProt A0A7E5W3Q7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 7 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts	Chain C； UniProt 1–156 Chain G； UniProt 1–156	Not recorded	H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） H/ACA ribonucleoprotein complex subunit × 1 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） RNA (97-MER) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.23 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YFO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YFL insect H/ACA snoRNP class I Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain C 1–156（156 aa） Chain G 1–156（156 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9YFM insect H/ACA snoRNP class II composite Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain C 1–156（156 aa） Chain G 1–156（156 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9YFN insect H/ACA snoRNP class III Deposited 2025-09-26	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain G 1–156（156 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7E5W3Q7_TRINI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–156； UniProt 1–156 Author chain G； PDBConstruct 1–156； UniProt 1–156

H/ACA ribonucleoprotein complex subunit 3

OrganismNot specified

UniProt A0A7E5W2Q0

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 7 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts	Chain F； UniProt 1–64 Chain H； UniProt 1–64	Not recorded	H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） H/ACA ribonucleoprotein complex subunit × 1 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） RNA (97-MER) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.23 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YFO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YFL insect H/ACA snoRNP class I Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain F 1–64（64 aa） Chain H 1–64（64 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9YFM insect H/ACA snoRNP class II composite Deposited 2025-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain F 1–64（64 aa） Chain H 1–64（64 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9YFN insect H/ACA snoRNP class III Deposited 2025-09-26	Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain F 1–64（64 aa） Chain H 1–64（64 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7E5W2Q0_TRINI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–64； UniProt 1–64 Author chain H； PDBConstruct 1–64； UniProt 1–64

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yfo
Deposition date deposition_date	2025-09-26
Structure title title	insect H/ACA snoRNP class IV
Keywords keywords	Pseudouridine synthase, enzyme complex, snoRNA, snoRNP, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.84 Å
Radius of gyration Rg (electron density) rg_electron	38.48 Å
Forward intensity I(0) i0	501388000.00
Molecular weight molecular_weight	163410.0 kDa
Excluded volume excluded_volume	196520 Å³
Envelope volume envelope_volume	272180 Å³
Hydration-shell volume shell_volume	57963 Å³
Envelope diameter envelope_diameter	131.3 Å
Shell Rg shell_rg	45.42 Å
Envelope Rg envelope_rg	37.72 Å
Shape Rg shape_rg	38.42 Å
Total Rg total_rg	39.02 Å
Total atoms total_atoms	21932
Residues n_residues	1264
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.5 Å
Rg (real space) rg_real	39.65 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	5.0140e+08
I(0) uncertainty (real space) i0_real_error	7.7140e+06
Rg (reciprocal space) rg_reciprocal	39.77 Å
I(0) (reciprocal space) i0_reciprocal	501400000.0000
Solution quality estimate total_estimate	0.9004
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.2 Å
Skewness Skewness skewness	0.151
Kurtosis Kurtosis kurtosis	-0.544
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31920000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	H/ACA ribonucleoprotein complex subunit 4-like
Molecular weight formula_weight	57643.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	21932

MTEVLQPGAEVFSEKKKKKVKESKEGVSLGQFQKLGDFKIEPTESVTKLDTAYWPLLLKNFDRLNVRTNHYTPLPFGHSPLKRPIAEYVKAGFINVDKPSNPSSHEVVSWIKRILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQNAGKEYVAVFSLHSAVENVKKVTQGLEKLRGALFQRPPLISAVKRQLRVRSVYDSKLLDFDKDRNIGVFWVSCEAGSYIRTMCVHLGLMLGVGGQMIELRRVRSGIQGEKEGMVTMHDILDAQWAYENHKDESYLRRVIKPLEGLLVAHKRIFIKDSAVNAVCYGAKVLLPGILRYEDGIEIDQEIVIVTTKGEAVALAIALMTTSTMASCDHGVAAKLKRVIMERDTYPRKWGLGPKASHKKSLISQGKLDKFGKPNENTPSEWLNSYVDYKKKDTNGDAEDDVGRKRTASTANADDPDNSVEVKSEKKKKKKKRDSEAADAVPEDGSGDATMEAETTTEADSSIRKEKKKKKKKDREQERVDE

Entity 2 Entity 2 polymer

Description description	H/ACA ribonucleoprotein complex subunit
Molecular weight formula_weight	22800.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSFRGRGGGGGGRGGYGGGGGGGGRGFGGRGGGGGRGGFGGRGGGRGGRGGGGGGFRQQDQGPPESVIPLGHYGWTVQDDLICKVDIEDVPYFNAPIFLENKEQIGKIDEIFGNLRDYFVSVKMGDNFKANSFKDGQQFYIDPAKLLPLKRFLPQPPGAKRGGGRGRGGPRGGRGGGGGFGRGGGGGGRGGGFGRGGGGGRGGFGRGGGGGYGGGGGGFNRGGGGFRGGRGGR

Entity 3 Entity 3 polymer

Description description	H/ACA ribonucleoprotein complex subunit 2-like protein
Molecular weight formula_weight	17704.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MGKIKQEPVEQEDQADVSVKNEPQSYDEKVDHCSVIAKPMAPKKLSKKIYKLIKKSTSHKNYIRNGLKIVQKQLRLGEKGIVFFAGDISPIEIMCHLPAVCEEKDIPYCYTPSRKDIGAAMGTMRGCVMVLVKEHDDYKDLFDEVRGEIKLLGHPI

Entity 4 Entity 4 polymer

Description description	H/ACA ribonucleoprotein complex subunit 3
Molecular weight formula_weight	7607.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

MYLRYYLNENGDRQYTLATIDPYGKPTISAHPARFSPEDKYSRHRIIIKKRFGLLLTQQPEPIL

Entity 5 Entity 5 polymer

Description description	RNA (97-MER)
Molecular weight formula_weight	44371.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CCUGCGGCAAAAAAAGUGCACGUCCCAAAACUGGGACGUGCACCAAAAAAAAGGCCGCAGGAACAGCAACGGAGCGAGUAAAAAAAAUGCACGUCCCAAAACUGGGACGUGCACAAAAAAAAAACUCGCUCACACAU

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.23 Å
Resolution测定方法 resolution_method	—
颗粒数 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

H/ACA ribonucleoprotein complex subunit 4-like

State in the Current Structure

Other States of the Same Protein in the Database

H/ACA ribonucleoprotein complex subunit

State in the Current Structure

Other States of the Same Protein in the Database

H/ACA ribonucleoprotein complex subunit 2-like protein

State in the Current Structure

Other States of the Same Protein in the Database

H/ACA ribonucleoprotein complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)