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- PDB-7bah: Structure of RIG-I CTD bound to OH-RNA -

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Basic information

Entry
Database: PDB / ID: 7bah
TitleStructure of RIG-I CTD bound to OH-RNA
Components
  • Antiviral innate immune response receptor RIG-I
  • RNA (5'-R(*GP*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 / cellular response to exogenous dsRNA / response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / bicellular tight junction / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / positive regulation of tumor necrosis factor production / double-stranded RNA binding / gene expression / TRAF3-dependent IRF activation pathway / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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 / Death-like domain superfamily ...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 / DEAD/DEAH box helicase domain / 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: 1.89 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

Downloads & links

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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(*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
D: RNA (5'-R(*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4066
Polymers37,2754
Non-polymers1312
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-21 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.920, 81.920, 111.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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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.: 2
Source method: isolated from a genetically manipulated source
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(*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')


Mass: 3827.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl pH 8.0 0.2 M NaCl 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→43.92 Å / Num. obs: 33784 / % possible obs: 99.4 % / Redundancy: 10.9 % / Rrim(I) all: 0.117 / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 10.9 % / Num. unique obs: 0 / Rrim(I) all: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NCU

3ncu


Resolution: 1.89→43.92 Å / Cross valid method: FREE R-VALUE / σ(F): 18.66 / Phase error: 31.2474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 1694 5.02 %
Rwork0.1948 32075 -
obs0.1969 33769 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.42 Å2
Refinement stepCycle: LAST / Resolution: 1.89→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 506 2 227 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352635
X-RAY DIFFRACTIONf_angle_d0.58963664
X-RAY DIFFRACTIONf_chiral_restr0.0419410
X-RAY DIFFRACTIONf_plane_restr0.0032376
X-RAY DIFFRACTIONf_dihedral_angle_d10.87544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.950.39581320.3482491X-RAY DIFFRACTION88.18
1.95-2.010.3191400.29252674X-RAY DIFFRACTION94.96
2.01-2.080.31621400.26662658X-RAY DIFFRACTION94.93
2.08-2.160.27331420.24852703X-RAY DIFFRACTION95.01
2.16-2.260.27311410.25372671X-RAY DIFFRACTION94.99
2.26-2.380.27441410.23892688X-RAY DIFFRACTION95.02
2.38-2.530.26191410.24612672X-RAY DIFFRACTION94.99
2.53-2.730.2511430.24112714X-RAY DIFFRACTION94.99
2.73-30.28851410.22722677X-RAY DIFFRACTION95
3-3.440.2171420.19392702X-RAY DIFFRACTION95.01
3.44-4.330.15511430.15442705X-RAY DIFFRACTION94.98
4.33-43.920.19681440.14582724X-RAY DIFFRACTION94.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.37487283338-0.111879536358-0.07626008707373.6696906002-0.99836686841.463542399820.0038973989162-0.151990602537-0.1627686487530.110796818791-0.165315453763-0.1691939194050.1124976143140.1153712401470.1538399794780.275394866080.001337315142510.01161791677610.3718193840430.04264736953380.135433854982-13.6552573411-24.99093787363.28566446002
22.807094150710.4972093844411.240394433021.488326059170.5962945675961.80568297753-0.06385123730840.07674352817460.0736900810317-0.197559329766-0.08426746473360.173775251604-0.0514716908463-0.09208032088410.1476506564760.3272590042270.0284791348955-0.02116668256050.304450268349-0.02423704861260.132276866102-12.5571882341-23.6155335676-38.3888630732
36.44876157878-1.138420541133.736936658161.11233608990.268846762097.924953469440.3002445689510.559878384335-0.620196599845-0.0326061220574-0.08417231450860.3214459324351.393509021310.0240627436145-0.2180093981690.648104646086-0.114248155858-0.0206483224820.4078340705740.01064387084330.319806261462-18.4714522004-32.4482959889-18.7673582123
44.58030383205-2.738296896432.540957457364.28218504605-3.565110194676.9282437213-0.0724108454593-0.385801240981-0.9029476717130.106882519580.502288255760.3106595470940.82639796333-0.791286800009-0.4239323593350.589804366688-0.0853665619003-0.02366773630440.3559951946440.03183891598260.387219956592-17.1290703098-33.1200873751-16.8485379087
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 803 through 923)AA803 - 9231 - 121
22(chain 'B' and resid 802 through 923)BB802 - 9231 - 122
33(chain 'C' and resid 1 through 12)CC1 - 12
44(chain 'D' and resid 1 through 12)DD1 - 12

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