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1yyw

Crystal structure of RNase III from Aquifex aeolicus complexed with double stranded RNA at 2.8-Angstrom Resolution

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonuclease III

Aquifex aeolicus

UniProt O67082

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 2 RNA 4 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3' × 4 water × 6 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 2 RNA 4 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3' × 4 water × 5 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1i4s 1jfz 1jfz 1rc5 1rc5

5 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1rc7 1yyk 1yyo 1yyw 1yyw 1yz9 2ez6 2nue 2nuf 2nug 4m2z 4m30

12 assemblies

View Construct and Data Evidence
UniProt name RNC_AQUAE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain D； PDBConstruct 1–221； UniProt 1–221

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_id1yyw
Deposition date deposition_date2005-02-25
Structure title titleCrystal structure of RNase III from Aquifex aeolicus complexed with double stranded RNA at 2.8-Angstrom Resolution
Keywords keywordsRibonuclease III, double-stranded RNA, RNA interference, endonucleolytic cleavage, HYDROLASE-RNA COMPLEX; HYDROLASE/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.

1yyw__assembly_1__model_1

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

Download this curve (.dat)

1yyw__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.

1yyw__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）32.44 Å
Rg (electron density)31.17 Å
Total Rg31.89 Å
Atom count4654
Residues486
Excluded volume80560 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1yyw__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1yyw__assembly_2__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 (3)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1yywa1
Class classa — All alpha proteins
Fold Fold folda.149 — RNase III domain-like
Superfamily Superfamily superfamilya.149.1 — RNase III domain-like
Family Family familya.149.1.1 — RNase III catalytic domain-like
Domain ID domain_idd1yywa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.50 — dsRBD-like
Superfamily Superfamily superfamilyd.50.1 — dsRNA-binding domain-like
Family Family familyd.50.1.1 — Double-stranded RNA-binding domain (dsRBD)
Domain ID domain_idd1yywb1
Class classa — All alpha proteins
Fold Fold folda.149 — RNase III domain-like
Superfamily Superfamily superfamilya.149.1 — RNase III domain-like
Family Family familya.149.1.1 — RNase III catalytic domain-like
Domain ID domain_idd1yywb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.50 — dsRBD-like
Superfamily Superfamily superfamilyd.50.1 — dsRNA-binding domain-like
Family Family familyd.50.1.1 — Double-stranded RNA-binding domain (dsRBD)
Domain ID domain_idd1yywc1
Class classa — All alpha proteins
Fold Fold folda.149 — RNase III domain-like
Superfamily Superfamily superfamilya.149.1 — RNase III domain-like
Family Family familya.149.1.1 — RNase III catalytic domain-like
Domain ID domain_idd1yywc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.50 — dsRBD-like
Superfamily Superfamily superfamilyd.50.1 — dsRNA-binding domain-like
Family Family familyd.50.1.1 — Double-stranded RNA-binding domain (dsRBD)
Domain ID domain_idd1yywd1
Class classa — All alpha proteins
Fold Fold folda.149 — RNase III domain-like
Superfamily Superfamily superfamilya.149.1 — RNase III domain-like
Family Family familya.149.1.1 — RNase III catalytic domain-like
Domain ID domain_idd1yywd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.50 — dsRBD-like
Superfamily Superfamily superfamilyd.50.1 — dsRNA-binding domain-like
Family Family familyd.50.1.1 — Double-stranded RNA-binding domain (dsRBD)

CATH v4.4 (8 domains)

Domain ID domain_id1yywA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
Homologous superfamily homologous superfamily10 — Ribonuclease III domain
Domain ID domain_id1yywA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1yywB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
Homologous superfamily homologous superfamily10 — Ribonuclease III domain
Domain ID domain_id1yywB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1yywC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
Homologous superfamily homologous superfamily10 — Ribonuclease III domain
Domain ID domain_id1yywC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1yywD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1520 — Ribonuclease iii, N-terminal Endonuclease Domain; Chain A
Homologous superfamily homologous superfamily10 — Ribonuclease III domain
Domain ID domain_id1yywD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
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7. Citations (1)