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9lou

LGP2:dsRNA complex

Method: ELECTRON MICROSCOPY Dmax: 84.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent RNA helicase DHX58

Homo sapiens

UniProt Q96C10

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Monomer Protein × 1 RNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–678 Not recorded RNA × 1 RNA × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.36 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9LOU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2RQA Solution structure of LGP2 CTD Deposited 2009-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 546–678（133 aa） Fragment：UNP residues 546-678
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.25；Pressure ambient
NMR sample composition 1mM [U-100% 13C; U-100% 15N] LGP2, 50mM TRIS-2, 250mM sodium chloride-3, 1mM DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W4R Crystal structure of the regulatory domain of human LGP2 Deposited 2008-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 537–678（142 aa） Fragment：REGULATORY DOMAIN, RESIDUES 537-678
Not recorded HG MERCURY (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.60 Å R-free 0.266
2W4R Crystal structure of the regulatory domain of human LGP2 Deposited 2008-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 537–678（142 aa） Fragment：REGULATORY DOMAIN, RESIDUES 537-678
Not recorded HG MERCURY (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.60 Å R-free 0.266
2W4R Crystal structure of the regulatory domain of human LGP2 Deposited 2008-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 537–678（142 aa） Fragment：REGULATORY DOMAIN, RESIDUES 537-678
Not recorded HG MERCURY (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.60 Å R-free 0.266
2W4R Crystal structure of the regulatory domain of human LGP2 Deposited 2008-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 537–678（142 aa） Fragment：REGULATORY DOMAIN, RESIDUES 537-678
Not recorded HG MERCURY (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.60 Å R-free 0.266
3EQT Crystal structure of human LGP2 C-terminal domain in complex with dsRNA Deposited 2008-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 541–678（138 aa） Fragment：LGP2 C-terminal domain (UNP residues 541 to 678)
Chain B 541–678（138 aa） Fragment：LGP2 C-terminal domain (UNP residues 541 to 678)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M ammonium sulfate, 16-18% PEG3350, 0.1 M Tris-HCl buffer, protein concentration 30 mg/ml, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.254
9LOV LGP2:MDA5:dsRNA filament Deposited 2025-01-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–678（678 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 ZN ZINC ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DHX58_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–678； UniProt 1–678

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9lou

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9lou
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9lou
Deposition date deposition_date2025-01-23
Structure title titleLGP2:dsRNA complex
Keywords keywordsInnate immune system, RNA receptor, Cryo-EM, IMMUNE SYSTEM, IMMUNE SYSTEM-RNA complex; IMMUNE SYSTEM/RNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.61 Å
Radius of gyration Rg (electron density) rg_electron27.32 Å
Forward intensity I(0) i0112779000.00
Molecular weight molecular_weight75800.0 kDa
Excluded volume excluded_volume91810 ų
Envelope volume envelope_volume119730 ų
Hydration-shell volume shell_volume36055 ų
Envelope diameter envelope_diameter87.0 Å
Shell Rg shell_rg35.11 Å
Envelope Rg envelope_rg27.02 Å
Shape Rg shape_rg27.36 Å
Total Rg total_rg27.95 Å
Total atoms total_atoms5280
Residues n_residues619
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax84.5 Å
Rg (real space) rg_real27.49 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real1.1280e+08
I(0) uncertainty (real space) i0_real_error1.6010e+06
Rg (reciprocal space) rg_reciprocal27.53 Å
I(0) (reciprocal space) i0_reciprocal112800000.0000
Solution quality estimate total_estimate0.9054
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1 Å
Skewness Skewness skewness0.231
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18670000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)