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2f8s

Crystal structure of Aa-Ago with externally-bound siRNA

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

Argonaute protein

Aquifex aeolicus

UniProt O67434

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Monomer Protein 1 RNA 2 5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*AP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3' × 2 water × 1 Consistent with all polymers
2 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1yvu 2f8s 2f8t 2nub

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2f8s 2f8t

2 assemblies

View Construct and Data Evidence
UniProt name O67434_AQUAE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–706； UniProt 1–706 Author chain B； PDBConstruct 1–706； UniProt 1–706

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_id2f8s
Deposition date deposition_date2005-12-03
Structure title titleCrystal structure of Aa-Ago with externally-bound siRNA
Keywords keywordsArgonaute, siRNA, RISC loading complex, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/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.

2f8s__assembly_1__model_1

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

Download this curve (.dat)

2f8s__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2f8s__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）35.90 Å
Rg (electron density)33.67 Å
Total Rg34.53 Å
Atom count6794
Residues748
Excluded volume119830 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2f8s__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2f8s__assembly_2__model_1 monomeric （1） 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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2f8sa1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.14 — PAZ domain
Family Family familyb.34.14.1 — PAZ domain
Domain ID domain_idd2f8sa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamilyc.44.3 — PIWI domain N-terminal-like
Family Family familyc.44.3.1 — PIWI domain N-terminal
Domain ID domain_idd2f8sa4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.15 — PIWI domain C-terminal
Domain ID domain_idd2f8sb1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.14 — PAZ domain
Family Family familyb.34.14.1 — PAZ domain
Domain ID domain_idd2f8sb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamilyc.44.3 — PIWI domain N-terminal-like
Family Family familyc.44.3.1 — PIWI domain N-terminal
Domain ID domain_idd2f8sb4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.15 — PIWI domain C-terminal

CATH v4.4 (6 domains)

Domain ID domain_id2f8sA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology340 — PAZ domain fold
Homologous superfamily homologous superfamily10 — PAZ domain superfamily
Domain ID domain_id2f8sA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2f8sA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2f8sB02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology340 — PAZ domain fold
Homologous superfamily homologous superfamily10 — PAZ domain superfamily
Domain ID domain_id2f8sB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2f8sB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
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7. Citations (1)