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- PDB-7bai: Structure of RIG-I CTD (I875A) bound to p-RNA -

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Basic information

Entry
Database: PDB / ID: 7bai
TitleStructure of RIG-I CTD (I875A) bound to p-RNA
Components
  • Antiviral innate immune response receptor RIG-I
  • RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
KeywordsIMMUNE SYSTEM / RNA recognition / innate immunity
Function / homology
Function and homology information


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain ...RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsAnand, K. / Hagelueken, G. / Fusshoeller, D. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC2151-390873048 Germany
CitationJournal: To Be Published
Title: A conserved isoleucine in the RNA sensor RIG-I controls immune tolerance to mitochondrial RNA
Authors: de Regt, A.K. / Anand, K. / Gatterdam, K. / Hagelueken, G. / Hartmann, G. / Geyer, M. / Schlee, M.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antiviral innate immune response receptor RIG-I
B: Antiviral innate immune response receptor RIG-I
C: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
D: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
E: Antiviral innate immune response receptor RIG-I
V: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,48011
Polymers56,1536
Non-polymers3275
Water00
1
A: Antiviral innate immune response receptor RIG-I
B: Antiviral innate immune response receptor RIG-I
C: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
D: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5666
Polymers37,4354
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-19 kcal/mol
Surface area16560 Å2
MethodPISA
2
E: Antiviral innate immune response receptor RIG-I
V: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
hetero molecules

E: Antiviral innate immune response receptor RIG-I
V: RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,82810
Polymers37,4354
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4200 Å2
ΔGint-21 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.523, 135.126, 110.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Antiviral innate immune response receptor RIG-I / DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / ...DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 14810.255 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This is the I875A mutant of RIG-I / Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O95786, RNA helicase
#2: RNA chain RNA (5'-R(*(GDP)P*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')


Mass: 3907.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M thiocyanate pH 8.4 20% PEG 3350 10% ethylene glycol 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.3→43.72 Å / Num. obs: 8984 / % possible obs: 99.7 % / Redundancy: 13.4 % / Rrim(I) all: 0.27 / Net I/σ(I): 6.3
Reflection shellResolution: 3.3→3.35 Å / Num. unique obs: 0 / Rrim(I) all: 1.24

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NCU

3ncu


Resolution: 3.4→43.7 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 896 9.99 %
Rwork0.2183 --
obs0.2238 8971 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 771 5 0 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043891
X-RAY DIFFRACTIONf_angle_d0.9565412
X-RAY DIFFRACTIONf_dihedral_angle_d14.881540
X-RAY DIFFRACTIONf_chiral_restr0.055606
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.610.47971460.4135726X-RAY DIFFRACTION100
3.61-3.890.36981480.31321316X-RAY DIFFRACTION100
3.89-4.280.32231430.24031339X-RAY DIFFRACTION100
4.28-4.90.26241470.18531334X-RAY DIFFRACTION100
4.9-6.170.31571540.22561362X-RAY DIFFRACTION100
6.18-43.720.21551580.18541410X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.6677 Å / Origin y: -16.2101 Å / Origin z: 18.3622 Å
111213212223313233
T1.1057 Å20.191 Å2-0.0493 Å2-1.2404 Å20.0637 Å2--1.3356 Å2
L2.952 °21.4628 °2-0.8905 °2-1.3102 °2-0.1781 °2--3.5106 °2
S-0.1204 Å °-0.3094 Å °-0.5512 Å °-0.0471 Å °-0.1828 Å °-0.4108 Å °0.0046 Å °0.4204 Å °0.3068 Å °
Refinement TLS groupSelection details: all

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