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5f9f

Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

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 Homooligomer Protein 6 RNA 6 ;RNA (5'-R(*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3') ; × 6 ZINC ION × 6 MAGNESIUM ION × 6 TRIFLUOROETHANOL × 4 (R,R)-2,3-BUTANEDIOL × 13 water × 12 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 O95786-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–695； UniProt 187–880 Author chain C； PDBConstruct 2–695； UniProt 187–880 Author chain E； PDBConstruct 2–695； UniProt 187–880 Author chain G； PDBConstruct 2–695； UniProt 187–880 Author chain I； PDBConstruct 2–695； UniProt 187–880 Author chain K； PDBConstruct 2–695； UniProt 187–880

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_id5f9f
Deposition date deposition_date2015-12-09
Structure title titleCrystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA
Keywords keywordsComplex, RIG-I, capped RNA, self versus non-self, innate immunity, 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.

5f9f__assembly_1__model_1

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

Download this curve (.dat)

5f9f__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5f9f__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）59.21 Å
Rg (electron density)58.77 Å
Total Rg58.87 Å
Atom count34792
Residues4172
Excluded volume612440 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5f9f__assembly_1__model_1 dodecameric （12） 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 (7)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id5f9fA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fA04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
Domain ID domain_id5f9fC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fC03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fC04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
Domain ID domain_id5f9fE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fE03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fE04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
Domain ID domain_id5f9fG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fG03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fG04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
Domain ID domain_id5f9fI01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fI02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fI03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fI04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
Domain ID domain_id5f9fK01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fK02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5f9fK03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f9fK04
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily30 — RIG-I-like receptor, C-terminal regulatory domain
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7. Citations (1)