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6kyv

Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs

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

Probable ATP-dependent RNA helicase DDX58

Homo sapiens

UniProt O95786

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers
2 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers
3 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers
4 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers
5 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers
6 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2lwd 2lwe 2qfb 2qfb 2qfb 2qfb 2qfb 2qfb 2qfb 2qfb 2qfb 2qfb

25 assemblies; showing the first 12

Homodimer
4on9

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ykg 3lrn 3lrr 3ncu 3og8 3zd6 3zd7 4ay2 4bpb 4nqk 4p4h 5e3h

45 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DDX58_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–684； UniProt 242–922 Author chain D； PDBConstruct 4–684； UniProt 242–922 Author chain F； PDBConstruct 4–684； UniProt 242–922 Author chain H； PDBConstruct 4–684； UniProt 242–922 Author chain J； PDBConstruct 4–684； UniProt 242–922 Author chain L； PDBConstruct 4–684； UniProt 242–922

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_id6kyv
Deposition date deposition_date2019-09-20
Structure title titleCrystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs
Keywords keywordsRIG-I, DDX58, dsRNA, Wobble base pair, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

6kyv__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6kyv__assembly_4__model_1 | I(q)

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

6kyv__assembly_4__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）28.00 Å
Rg (electron density)27.54 Å
Total Rg28.27 Å
Atom count5795
Residues694
Excluded volume102160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6kyv__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6kyv__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6kyv__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6kyv__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6kyv__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6kyv__assembly_6__model_1 dimeric （2） 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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7. Citations (1)