2hvy

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus

Method: X-RAY DIFFRACTION

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

Probable tRNA pseudouridine synthase B

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	H/ACA RNA × 1 Small nucleolar rnp similar to gar1 × 1 （Q8U029） Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） 50S ribosomal protein L7Ae × 1 （Q8U160） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRUB_PYRFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–340； UniProt 1–340

Small nucleolar rnp similar to gar1

Pyrococcus furiosus

UniProt Q8U029

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	H/ACA RNA × 1 Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） 50S ribosomal protein L7Ae × 1 （Q8U160） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U029_PYRFU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–104； UniProt 1–104

Ribosome biogenesis protein Nop10

Pyrococcus furiosus

UniProt Q8U1R4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	H/ACA RNA × 1 Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） Small nucleolar rnp similar to gar1 × 1 （Q8U029） 50S ribosomal protein L7Ae × 1 （Q8U160） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOP10_PYRFU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–60； UniProt 1–60

50S ribosomal protein L7Ae

Pyrococcus furiosus

UniProt Q8U160

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	H/ACA RNA × 1 Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） Small nucleolar rnp similar to gar1 × 1 （Q8U029） Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL7A_PYRFU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 2–124； UniProt 1–123

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	2hvy
Deposition date deposition_date	2006-07-31
Structure title title	Crystal structure of an H/ACA box RNP from Pyrococcus furiosus
Keywords keywords	H/ACA RNA, RNP, PSEUDOURIDINE synthase, Guide RNA, ISOMERASE-BIOSYNTHETIC PROTEIN-RNA COMPLEX; ISOMERASE/BIOSYNTHETIC PROTEIN/RNA
Experimental Method method	X-RAY DIFFRACTION

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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.

2hvy__assembly_1__model_1

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

Download this curve (.dat)

2hvy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hvy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.68 Å
Rg (electron density)	30.23 Å
Total Rg	30.82 Å
Atom count	5779
Residues	629
Excluded volume	99539 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hvy__assembly_1__model_1`	pentameric （5）	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 (8)

Entity 1 Entity 1 polymer

Description description	H/ACA RNA
Molecular weight formula_weight	21021.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	5897

GGGUCCGCCUUGAGUGCCCGGGUGAGAAGCAUGAUCCCGGGUAAUUAUGGCGGACCCACAGAAUU

Entity 2 Entity 2 polymer

Description description	Probable tRNA pseudouridine synthase B
Molecular weight formula_weight	39453.9 kDa
EC 编号 ec_number	5.4.99.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MARDEVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEKRDRSHHHHHH

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Small nucleolar rnp similar to gar1
Molecular weight formula_weight	12340.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEKQGEKMKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDERKRKESPKKNKEKRMKKKKRLNR

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ribosome biogenesis protein Nop10
Molecular weight formula_weight	7214.6 kDa
Mutation mutation	R2K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKFRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGIGRKEK

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	50S ribosomal protein L7Ae
Molecular weight formula_weight	14314.6 kDa
Mutation mutation	M2A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMKHHHHHH

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2hvya1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d2hvya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.2 — Pseudouridine synthase II TruB

Domain ID domain_id	d2hvyb1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.5 — Gar1-like SnoRNP

Domain ID domain_id	d2hvyc1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.16 — Nop10-like SnoRNP
Family Family family	g.41.16.1 — Nucleolar RNA-binding protein Nop10-like

Domain ID domain_id	d2hvyd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.3 — L30e-like
Family Family family	d.79.3.1 — L30e/L7ae ribosomal proteins

CATH v4.4 (5 domains)

Domain ID domain_id	2hvyA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	10 — PUA domain

Domain ID domain_id	2hvyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2350 — Pseudouridine synthase
Homologous superfamily homologous superfamily	10 — Pseudouridine synthase

Domain ID domain_id	2hvyB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	230 — Probable tRNA pseudouridine synthase domain

Domain ID domain_id	2hvyC00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	40 — H/ACA ribonucleoprotein complex, subunit Nop10

Domain ID domain_id	2hvyD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

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Unit-cell length a length_a	83.031 Å
Unit-cell length b length_b	90.950 Å
Unit-cell length c length_c	114.064 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2398
R_work r_work	0.2379
R_free r_free	0.2781

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus

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

Probable tRNA pseudouridine synthase B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nucleolar rnp similar to gar1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosome biogenesis protein Nop10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L7Ae

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

2hvy__assembly_1__model_1

2hvy__assembly_1__model_1 | I(q)

2hvy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)