SAXSdb — 9yfm

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

H/ACA ribonucleoprotein complex subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） RNA (96-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

H/ACA ribonucleoprotein complex subunit 2-like protein

OrganismNot specified

UniProt A0A7E5W3Q7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	H/ACA ribonucleoprotein complex subunit × 2 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） RNA (96-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7E5W3Q7_TRINI
Isoform	—
PDB entities	2
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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	H/ACA ribonucleoprotein complex subunit × 2 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） H/ACA ribonucleoprotein complex subunit 4-like × 2 （A0A7E5VBG0） RNA (96-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7E5W2Q0_TRINI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–64； UniProt 1–64 Author chain H； PDBConstruct 1–64； UniProt 1–64

H/ACA ribonucleoprotein complex subunit 4-like

OrganismNot specified

UniProt A0A7E5VBG0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	H/ACA ribonucleoprotein complex subunit × 2 （A0A7E5WAP8） H/ACA ribonucleoprotein complex subunit 2-like protein × 2 （A0A7E5W3Q7） H/ACA ribonucleoprotein complex subunit 3 × 2 （A0A7E5W2Q0） RNA (96-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7E5VBG0_TRINI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–514； UniProt 1–514 Author chain D； PDBConstruct 1–514； UniProt 1–514

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

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9yfm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9yfm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yfm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	41.81 Å
Rg (electron density)	41.13 Å
Total Rg	41.40 Å
Atom count	22920
Residues	1321
Excluded volume	205170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yfm__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	H/ACA ribonucleoprotein complex subunit
Molecular weight formula_weight	22800.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E
Atom count atom_count	22920

MSFRGRGGGGGGRGGYGGGGGGGGRGFGGRGGGGGRGGFGGRGGGRGGRGGGGGGFRQQDQGPPESVIPLGHYGWTVQDDLICKVDIEDVPYFNAPIFLENKEQIGKIDEIFGNLRDYFVSVKMGDNFKANSFKDGQQFYIDPAKLLPLKRFLPQPPGAKRGGGRGRGGPRGGRGGGGGFGRGGGGGGRGGGFGRGGGGGRGGFGRGGGGGYGGGGGGFNRGGGGFRGGRGGR

Entity 2 Entity 2 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 3 Entity 3 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 4 Entity 4 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

MTEVLQPGAEVFSEKKKKKVKESKEGVSLGQFQKLGDFKIEPTESVTKLDTAYWPLLLKNFDRLNVRTNHYTPLPFGHSPLKRPIAEYVKAGFINVDKPSNPSSHEVVSWIKRILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQNAGKEYVAVFSLHSAVENVKKVTQGLEKLRGALFQRPPLISAVKRQLRVRSVYDSKLLDFDKDRNIGVFWVSCEAGSYIRTMCVHLGLMLGVGGQMIELRRVRSGIQGEKEGMVTMHDILDAQWAYENHKDESYLRRVIKPLEGLLVAHKRIFIKDSAVNAVCYGAKVLLPGILRYEDGIEIDQEIVIVTTKGEAVALAIALMTTSTMASCDHGVAAKLKRVIMERDTYPRKWGLGPKASHKKSLISQGKLDKFGKPNENTPSEWLNSYVDYKKKDTNGDAEDDVGRKRTASTANADDPDNSVEVKSEKKKKKKKRDSEAADAVPEDGSGDATMEAETTTEADSSIRKEKKKKKKKDREQERVDE

Entity 5 Entity 5 polymer

Description description	RNA (96-MER)
Molecular weight formula_weight	30928.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CCUGCGGCGUGCACGUCCCAACUGGGACGUGCACCGGCCGCAGGAACAGCAACGGAGCGAUGCACGUCCCAACUGGGACGUGCACCGCUCACACAU

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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	2.95 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	733250

insect H/ACA snoRNP class II composite

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

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

H/ACA ribonucleoprotein complex subunit 4-like

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yfm__assembly_1__model_1

9yfm__assembly_1__model_1 | I(q)

9yfm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

7. Citations (1)

insect H/ACA snoRNP class II composite

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

H/ACA ribonucleoprotein complex subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 2-like protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 4-like

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yfm__assembly_1__model_1

9yfm__assembly_1__model_1 | I(q)

9yfm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

7. Citations (1)