SAXSdb — 2rfk

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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 3 RNA 3	guide RNA 1 × 1 guide RNA 2 × 1 target RNA × 1 Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） Small nucleolar rnp similar to gar1 × 1 （Q8U029） ZINC ION × 1	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	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–334； UniProt 5–338

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 3	guide RNA 1 × 1 guide RNA 2 × 1 target RNA × 1 Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） Small nucleolar rnp similar to gar1 × 1 （Q8U029） ZINC ION × 1	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	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–53； UniProt 3–55

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 3 RNA 3	guide RNA 1 × 1 guide RNA 2 × 1 target RNA × 1 Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） ZINC ION × 1	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	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–74； UniProt 8–81

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	2rfk
Deposition date deposition_date	2007-09-30
Structure title title	Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex
Keywords keywords	;PROTEIN-RNA COMPLEX, Archaeal H-ACA Ribonucleoprotein Complex, Isomerase, tRNA processing, Ribosome biogenesis, rRNA processing, Isomerase-RNA COMPLEX, Structural Genomics, Southeast Collaboratory for Structural Genomics, SECSG, PSI-2, Protein Structure Initiative ;; 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.

2rfk__assembly_1__model_1

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

Download this curve (.dat)

2rfk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rfk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.04 Å
Rg (electron density)	28.30 Å
Total Rg	28.97 Å
Atom count	5005
Residues	522
Excluded volume	85434 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rfk__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	guide RNA 1
Molecular weight formula_weight	6797.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	5005

GGGCUCCGGAAACCGCGGCGC

Entity 2 Entity 2 polymer

Description description	guide RNA 2
Molecular weight formula_weight	8229.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

GCGCUUCGCUCCCGGAGCCCACACUA

Entity 3 Entity 3 polymer

Description description	target RNA
Molecular weight formula_weight	4535.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

GGAGCGUGCGGUUU

Entity 4 Entity 4 polymer

Description description	Probable tRNA pseudouridine synthase B
Molecular weight formula_weight	37862.2 kDa
EC 编号 ec_number	5.4.99.-
Mutation mutation	D85A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

EVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEKRD

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	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 6 Entity 6 polymer

Description description	Small nucleolar rnp similar to gar1
Molecular weight formula_weight	8515.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDE

Source Source

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

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

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2rfka1
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	d2rfka2
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	d2rfkb_
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	d2rfkc_
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

CATH v4.4 (4 domains)

Domain ID domain_id	2rfkA01
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	2rfkA02
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	2rfkB00
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	2rfkC00
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

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Unit-cell length a length_a	96.561 Å
Unit-cell length b length_b	96.561 Å
Unit-cell length c length_c	240.978 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.870 Å
Low-resolution limit resolution_low	42.520 Å
R factor r_factor	0.2503
R_work r_work	0.2478
R_free r_free	0.3004

Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2rfk__assembly_1__model_1

2rfk__assembly_1__model_1 | I(q)

2rfk__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 (7)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)