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6gpg

Structure of the RIG-I Singleton-Merten syndrome variant C268F

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 2 ;RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3') ; × 2 ZINC ION × 1 MAGNESIUM 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 A； PDBConstruct 21–714； UniProt 232–925

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_id6gpg
Deposition date deposition_date2018-06-05
Structure title titleStructure of the RIG-I Singleton-Merten syndrome variant C268F
Keywords keywordsinnate immune system, RIG-I, Singleton-Merten syndrome, RNA-dependent ATPase, RNA binding protein, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
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.

6gpg__assembly_1__model_1

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

Download this curve (.dat)

6gpg__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.

6gpg__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）28.16 Å
Rg (electron density)27.78 Å
Total Rg28.48 Å
Atom count5812
Residues677
Excluded volume102300 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6gpg__assembly_1__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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6gpgA01
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_id6gpgA02
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_id6gpgA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id6gpgA04
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)