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5f98

Crystal structure of RIG-I in complex with Cap-0 RNA

Method: X-RAY DIFFRACTION Dmax: 198.7 Å Quality: GOOD
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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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Homooligomer Protein × 6 RNA 6 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain A； UniProt 232–925 Chain C； UniProt 232–925 Chain E； UniProt 232–925 Chain G； UniProt 232–925 Chain I； UniProt 232–925 Chain K； UniProt 232–925 Not recorded ;RNA (5'-R(P*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 ZN ZINC ION × 6 MG MAGNESIUM ION × 6 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% (w/v) PEG 3350, 0.2 M NaSCN, 100 mM MOPS (pH 7.8), 3.5% (v/v) 2,2,2-trifluoroethanol Resolution 3.28 Å R-free 0.277

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 5F98 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LWD Solution structure of second CARD of human RIG-I Deposited 2012-07-27 Different construct Different mutation/modification 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 95–190（96 aa） Fragment：CARD 2 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient
NMR sample composition 300 uM [U-100% 15N] card2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 100% D2O | 100% D2O
Resolution not provided
2LWE Solution structure of mutant (T170E) second CARD of human RIG-I Deposited 2012-07-27 Different construct Different mutation/modification 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 95–190（96 aa） Fragment：CARD 2 domain
Mutation：T170E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient
NMR sample composition 300 uM [U-100% 15N] card2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 100% D2O | 100% D2O
Resolution not provided
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 802–925（124 aa） Fragment：Regulatory domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.285
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2QFD Crystal structure of the regulatory domain of human RIG-I with bound Hg Deposited 2007-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 802–925（124 aa） Fragment：Regulatory domain
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.276
2RMJ Solution structure of RIG-I C-terminal domain Deposited 2007-10-23 Different construct Different mutation/modification 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 792–925（134 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 0.25
NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] RIG-I, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2YKG Structural insights into RNA recognition by RIG-I Deposited 2011-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 230–925（696 aa） Fragment：RESIDUES 230-925
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000
Resolution 2.50 Å R-free 0.273
3LRN Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA Deposited 2010-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 803–923（121 aa） Fragment：human RIG-I CTD
Chain B 803–923（121 aa） Fragment：human RIG-I CTD
Mutation：C829S Mutation：C829S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；15% PEG 3,350, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.282
3LRR Crystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ppp dsRNA Deposited 2010-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 803–923（121 aa） Fragment：RIG-I CTD (UNP residues 803 to 923)
Chain B 803–923（121 aa） Fragment：RIG-I CTD (UNP residues 803 to 923)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 3,350 (15%) plus ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.228
3NCU Structural and functional insights into pattern recognition by the innate immune receptor RIG-I Deposited 2010-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 792–925（134 aa） Fragment：residues 792-925
Chain B 792–925（134 aa） Fragment：residues 792-925
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27% (v/v) polyethylene glycerol 3350 (PEG 3350), 50 mM Tris-HCl, pH 7.5, 0.1 M KCl, and 10 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.55 Å R-free 0.229
3OG8 Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA Deposited 2010-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 802–925（124 aa） Fragment：C-terminal domain
Chain B 802–925（124 aa） Fragment：C-terminal domain
Mutation：C829S Mutation：C829S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27% PEG MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.278
3ZD6 Snapshot 1 of RIG-I scanning on RNA duplex Deposited 2012-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 185–880（696 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；pH 9
Resolution 2.80 Å R-free 0.279
3ZD7 Snapshot 3 of RIG-I scanning on RNA duplex Deposited 2012-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 185–880（696 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；pH 9
Resolution 2.50 Å R-free 0.288
4AY2 Capturing 5' tri-phosphorylated RNA duplex by RIG-I Deposited 2012-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 239–925（687 aa） Fragment：RESIDUES 239-925
Not recorded ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.286
4BPB STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I Deposited 2013-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 230–925（696 aa） Fragment：RESIDUES 230-925
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000
Resolution 2.58 Å R-free 0.255
4NQK Structure of an Ubiquitin complex Deposited 2013-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200
Chain B 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200
Chain C 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200
Chain D 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG3350, 0.2 M Tri-Li Citrate, 3% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.70 Å R-free 0.285
4ON9 DECH box helicase domain Deposited 2014-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–793（564 aa） Fragment：UNP residues 230-793
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.71 Å R-free 0.258
4ON9 DECH box helicase domain Deposited 2014-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–793（564 aa） Fragment：UNP residues 230-793
Not recorded SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.71 Å R-free 0.258
4ON9 DECH box helicase domain Deposited 2014-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 230–793（564 aa） Fragment：UNP residues 230-793
Chain B 230–793（564 aa） Fragment：UNP residues 230-793
Not recorded SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.71 Å R-free 0.258
4P4H Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain Deposited 2014-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain A 1–201（201 aa）
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Chain E 1–201（201 aa）
Chain F 1–201（201 aa）
Chain G 1–201（201 aa）
Chain H 1–201（201 aa）
Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Tri-Li Citrate, PEG 3350, Cr(III) Cl3
Resolution 3.40 Å R-free 0.240
5E3H Structural Basis for RNA Recognition and Activation of RIG-I Deposited 2015-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 232–925（694 aa） Fragment：UNP residues 232-925
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% w/v PEG3350, 0.25 M sodium thiocyanate, 100 mM MOPS, pH 7.8, 3% v/v 2,2,2-trifluoroethanol
Resolution 2.70 Å R-free 0.268
5F9F Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA Deposited 2015-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: dodecameric
Chain A 187–880（694 aa）
Chain C 187–880（694 aa）
Chain E 187–880（694 aa）
Chain G 187–880（694 aa）
Chain I 187–880（694 aa）
Chain K 187–880（694 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 ETF TRIFLUOROETHANOL × 4 BU3 (R,R)-2,3-BUTANEDIOL × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；23% (w/v) PEG 3350, 0.3 M NaSCN, 100 mM MOPS (pH 7.8)
Resolution 2.60 Å R-free 0.259
5F9H Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA Deposited 2015-12-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: dodecameric
Chain A 232–925（694 aa）
Chain C 232–925（694 aa）
Chain E 232–925（694 aa）
Chain G 232–925（694 aa）
Chain I 232–925（694 aa）
Chain K 232–925（694 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；23% (w/v) PEG 3350, 0.25 M KSCN, 100 mM MOPS (pH 7.8)
Resolution 3.10 Å R-free 0.266
6GPG Structure of the RIG-I Singleton-Merten syndrome variant C268F Deposited 2018-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 232–925（694 aa）
Mutation：C268F ZN ZINC ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M MOPS pH 7.5, 17.5 % (w/v) PEG 3350, 0.25 M NaSCN, 3 % (v/v) 2,2,2 trifluoroethanol
Resolution 2.89 Å R-free 0.260
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain D 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain F 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain H 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain J 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain L 242–922（681 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic
Resolution 3.00 Å R-free 0.274
7BAH Structure of RIG-I CTD bound to OH-RNA Deposited 2020-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 802–925（124 aa）
Chain B 802–925（124 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；283.15 K；0.1 M Tris-HCl pH 8.0 0.2 M NaCl 18% PEG 3350
Resolution 1.89 Å R-free 0.224
7BAI Structure of RIG-I CTD (I875A) bound to p-RNA Deposited 2020-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 802–925（124 aa）
Chain B 802–925（124 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.2 M thiocyanate pH 8.4 20% PEG 3350 10% ethylene glycol 10% MPD
Resolution 3.40 Å R-free 0.273
7BAI Structure of RIG-I CTD (I875A) bound to p-RNA Deposited 2020-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain E 802–925（124 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.2 M thiocyanate pH 8.4 20% PEG 3350 10% ethylene glycol 10% MPD
Resolution 3.40 Å R-free 0.273
7JL1 Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer) Deposited 2020-07-29 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 Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 159–880（722 aa） Fragment：UNP residues 159-880
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7JL3 Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer) Deposited 2020-07-29 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 Heteromer；Protein × 6 PDB declaration: octameric
Chain A 159–880（722 aa） Fragment：UNP residues 159-880
Chain C 159–880（722 aa） Fragment：UNP residues 159-880
Chain E 159–880（722 aa） Fragment：UNP residues 159-880
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 ALF TETRAFLUOROALUMINATE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7MK1 Structure of a protein-modified aptamer complex Deposited 2021-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 801–925（125 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285.15 K；30% PEG3350, 0.01 M Na acetate pH 4.8
Resolution 1.90 Å R-free 0.220
7MK1 Structure of a protein-modified aptamer complex Deposited 2021-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 801–925（125 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285.15 K；30% PEG3350, 0.01 M Na acetate pH 4.8
Resolution 1.90 Å R-free 0.220
7TNX Cryo-EM structure of RIG-I in complex with p3dsRNA Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7TNY Cryo-EM structure of RIG-I in complex with p2dsRNA Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TNZ Cryo-EM structure of RIG-I in complex with p1dsRNA Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7TO0 Cryo-EM structure of RIG-I in complex with OHdsRNA Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7TO1 Cryo-EM structure of RIG-I bound to the end of p3SLR30 (+ATP) Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
7TO2 Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP) Deposited 2022-01-22 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8DVR Cryo-EM structure of RIG-I bound to the end of p3SLR30 (+AMPPNP) Deposited 2022-07-29 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8DVS Cryo-EM structure of RIG-I bound to the end of OHSLR30 (+ATP) Deposited 2022-07-29 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8DVU Cryo-EM structure of RIG-I bound to the internal sites of OHSLR30 (+ATP) Deposited 2022-07-29 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8G7T Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-end) Deposited 2023-02-17 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 Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–925（925 aa）
Chain C 1–925（925 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8G7U Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-semi-closed end) Deposited 2023-02-17 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 Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–925（925 aa）
Chain C 1–925（925 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8G7V Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-inter) Deposited 2023-02-17 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 Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–925（925 aa）
Chain C 1–925（925 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SCZ Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30 Deposited 2023-04-06 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8SD0 Cryo-EM structure of RIG-I in complex with p3SLR14 Deposited 2023-04-06 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9KTW Cryo-EM structure of wild type RIG-I with 5'p-RNA Deposited 2024-12-03 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–925（925 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；25mM HEPES, 150mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9KU4 Cryo-EM structure of E373A mutant RIG-I with 5'p-RNA Deposited 2024-12-03 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–925（925 aa）
Mutation：E373A ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；25mM HEPES, 150mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å

43 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDX58_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–695； UniProt 232–925 Author chain C； PDBConstruct 2–695； UniProt 232–925 Author chain E； PDBConstruct 2–695； UniProt 232–925 Author chain G； PDBConstruct 2–695； UniProt 232–925 Author chain I； PDBConstruct 2–695； UniProt 232–925 Author chain K； PDBConstruct 2–695； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5f98

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5f98
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5f98
Deposition date deposition_date2015-12-09
Structure title titleCrystal structure of RIG-I in complex with Cap-0 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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier59.30 Å
Radius of gyration Rg (electron density) rg_electron58.75 Å
Forward intensity I(0) i03528970000.00
Molecular weight molecular_weight468000.0 kDa
Excluded volume excluded_volume571300 ų
Envelope volume envelope_volume885810 ų
Hydration-shell volume shell_volume123400 ų
Envelope diameter envelope_diameter196.4 Å
Shell Rg shell_rg63.82 Å
Envelope Rg envelope_rg56.78 Å
Shape Rg shape_rg58.77 Å
Total Rg total_rg58.80 Å
Total atoms total_atoms32708
Residues n_residues4021
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 dmax198.7 Å
Rg (real space) rg_real59.07 Å
Rg uncertainty (real space) rg_real_error2.14 Å
I(0) (real space) i0_real3.5290e+09
I(0) uncertainty (real space) i0_real_error8.1590e+07
Rg (reciprocal space) rg_reciprocal59.47 Å
I(0) (reciprocal space) i0_reciprocal3531000000.0000
Solution quality estimate total_estimate0.8720
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary76.4 Å
Skewness Skewness skewness0.151
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha186400000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.836
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id5f98A01
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_id5f98A02
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_id5f98A03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98A04
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_id5f98C01
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_id5f98C02
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_id5f98C03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98C04
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_id5f98E01
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_id5f98E02
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_id5f98E03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98E04
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_id5f98G01
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_id5f98G02
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_id5f98G03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98G04
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_id5f98I01
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_id5f98I02
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_id5f98I03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98I04
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_id5f98K01
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_id5f98K02
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_id5f98K03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5f98K04
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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8. Citations (1)

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9. Files and Curves (10)