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3hk2

Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand

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

Argonaute

Thermus thermophilus

UniProt Q746M7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 DNA 1 RNA 1 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3' × 1 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' × 1 MAGNESIUM ION × 2 water × 1 Consistent with all polymers
2 Other combination Monomer Protein 1 DNA 1 RNA 1 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3' × 1 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' × 1 MAGNESIUM ION × 2 water × 2 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
3dlb 3dlh 3dlh 3f73 3f73 3hjf 3hk2 3hk2 3hm9 3ho1 3hvr 3hvr

31 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q746M7_THET2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–685； UniProt 1–685 Author chain B； PDBConstruct 1–685； UniProt 1–685

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_id3hk2
Deposition date deposition_date2009-05-22
Structure title titleCrystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand
Keywords keywordsargonaute, protein-DNA-RNA complex, NUCLEIC ACID BINDING PROTEIN-DNA-RNA COMPLEX; NUCLEIC ACID BINDING PROTEIN/DNA/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.

3hk2__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hk2__assembly_2__model_1 | I(q)

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

3hk2__assembly_2__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）28.19 Å
Rg (electron density)28.02 Å
Total Rg28.60 Å
Atom count5555
Residues698
Excluded volume96301 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3hk2__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3hk2__assembly_2__model_1 trimeric （3） 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) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id3hk2A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3hk2A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2620 —
Domain ID domain_id3hk2A03
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology260 — paz domain
Homologous superfamily homologous superfamily50 —
Domain ID domain_id3hk2A04
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_id3hk2A05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3hk2B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3hk2B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2620 —
Domain ID domain_id3hk2B03
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology260 — paz domain
Homologous superfamily homologous superfamily50 —
Domain ID domain_id3hk2B04
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_id3hk2B05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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7. Citations (1)