3hjw

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

Method: X-RAY DIFFRACTION

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

Pseudouridine synthase Cbf5

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 2	Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） 50S ribosomal protein L7Ae × 1 （Q8U160） RNA (58-MER) × 1 5'-R(GPAPGPCPGP(FHU)PGPCPGPGPUPUP*U)-3' × 1 ZINC ION × 1 POTASSIUM 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–327； UniProt 8–334

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 3 RNA 2	Pseudouridine synthase Cbf5 × 1 （Q7LWY0） 50S ribosomal protein L7Ae × 1 （Q8U160） RNA (58-MER) × 1 5'-R(GPAPGPCPGP(FHU)PGPCPGPGPUPUP*U)-3' × 1 ZINC ION × 1 POTASSIUM 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–53； UniProt 3–55

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 3 RNA 2	Pseudouridine synthase Cbf5 × 1 （Q7LWY0） Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） RNA (58-MER) × 1 5'-R(GPAPGPCPGP(FHU)PGPCPGPGPUPUP*U)-3' × 1 ZINC ION × 1 POTASSIUM 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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–120； UniProt 3–122

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	3hjw
Deposition date deposition_date	2009-05-22
Structure title title	Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Keywords keywords	;protein-RNA complex, Box H/ACA, ribonucleoprotein particles, RNP, pseudouridine synthase, pseudouridylase, pseudouridylation, RNA editing, post-transcriptional modification, Isomerase, tRNA processing, Ribonucleoprotein, Ribosome biogenesis, rRNA processing, Ribosomal protein, RNA-binding, ISOMERASE-RNA COMPLEX ;; ISOMERASE/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.

3hjw__assembly_1__model_1

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

Download this curve (.dat)

3hjw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hjw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.06 Å
Rg (electron density)	28.50 Å
Total Rg	29.15 Å
Atom count	5481
Residues	570
Excluded volume	93179 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hjw__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	Pseudouridine synthase Cbf5
Molecular weight formula_weight	36990.2 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
Atom count atom_count	5580

RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW

Source Source

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

Entity 2 Entity 2 polymer

Description description	Ribosome biogenesis protein Nop10
Molecular weight formula_weight	6352.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI

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	50S ribosomal protein L7Ae
Molecular weight formula_weight	13083.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELM

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	RNA (58-MER)
Molecular weight formula_weight	18687.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

GGGCCACGGAAACCGCGCGCGGUGAUCAAUGAGCCGCGUUCGCUCCCGUGGCCCACAA

Entity 5 Entity 5 polymer

Description description	5'-R(GPAPGPCPGP(FHU)PGPCPGPGPUPUP*U)-3'
Molecular weight formula_weight	4226.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

GAGCGUGCGGUUU

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 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	99

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3hjwa1
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.265.1.0 — automated matches

Domain ID domain_id	d3hjwa2
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.122.1.0 — automated matches

Domain ID domain_id	d3hjwb_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3hjwA01
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	3hjwA02
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	3hjwB00
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	3hjwC00
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	186.013 Å
Unit-cell length b length_b	63.026 Å
Unit-cell length c length_c	85.447 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	46.520 Å
R factor r_factor	0.2180
R_work r_work	0.2170
R_free r_free	0.2480

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

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

Pseudouridine synthase Cbf5

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

3hjw__assembly_1__model_1

3hjw__assembly_1__model_1 | I(q)

3hjw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)