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3hjy

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

UniProt Q7LWY0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 2 RNA 3 Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3' × 1 RNA (25-MER) × 1 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3' × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ey4 2ey4 2ey4 2hvy 2rfk 3hax 3hay 3hjw 3hjy 3lwo 3lwp 3lwq

15 assemblies; showing the first 12

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 2 RNA 3 pseudouridine synthase CBf5 × 1 （Q7LWY0） 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3' × 1 RNA (25-MER) × 1 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3' × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ey4 2ey4 2ey4 2hvy 2rfk 3hax 3hay 3hjw 3hjy 3lwo 3lwp 3lwq

15 assemblies; showing the first 12

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

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_id3hjy
Deposition date deposition_date2009-05-22
Structure title titleStructure 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, ISOMERASE-RNA COMPLEX ;; ISOMERASE/RNA
Experimental Method methodX-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.

3hjy__assembly_1__model_1

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

Download this curve (.dat)

3hjy__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3hjy__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）26.44 Å
Rg (electron density)25.35 Å
Total Rg26.18 Å
Atom count4260
Residues433
Excluded volume71965 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3hjy__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 (5)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3hjyA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily10 — PUA domain
Domain ID domain_id3hjyA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2350 — Pseudouridine synthase
Homologous superfamily homologous superfamily10 — Pseudouridine synthase
Domain ID domain_id3hjyB00
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily40 — H/ACA ribonucleoprotein complex, subunit Nop10
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7. Citations (1)