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- PDB-2ykg: Structural insights into RNA recognition by RIG-I -

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Basic information

Entry
Database: PDB / ID: 2ykg
TitleStructural insights into RNA recognition by RIG-I
Components
  • 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
KeywordsHYDROLASE / 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 / response to exogenous dsRNA / cellular 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 / double-stranded RNA binding / positive regulation of tumor necrosis factor production / gene expression / TRAF3-dependent IRF activation pathway / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / Ub-specific processing proteases / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / GTP binding / positive regulation of gene expression / 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
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Death-like domain superfamily / Beta Complex / 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsLuo, D. / Pyle, A.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural Insights Into RNA Recognition by Rig-I.
Authors: Luo, D. / Ding, S.C. / Vela, A. / Kohlway, A. / Lindenbach, B.D. / Pyle, A.M.
History
DepositionMay 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
C: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
D: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2585
Polymers86,0973
Non-polymers1612
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-48.5 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.618, 76.208, 219.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 / DEAD BOX PROTEIN 58 / RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN / RIG-1 / RETINOIC ACID-INDUCIBLE GENE ...DEAD BOX PROTEIN 58 / RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN / RIG-1 / RETINOIC ACID-INDUCIBLE GENE I PROTEIN / RIG-I


Mass: 79682.797 Da / Num. of mol.: 1 / Fragment: RESIDUES 230-925 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O95786, RNA helicase
#2: RNA chain 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'


Mass: 3206.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growpH: 9
Details: 0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 26861 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→45 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU B: 26.128 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.732 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 1341 5 %RANDOM
Rwork0.22036 ---
obs0.223 25452 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--1.53 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 424 6 99 5517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225567
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.0587622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53724.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12315898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9111522
X-RAY DIFFRACTIONr_chiral_restr0.090.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213987
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5331.53180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01225119
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33132387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1684.52503
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 23 -
Rwork0.363 649 -
obs--33.17 %
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)
11.4922-0.0862-0.74171.52350.41081.9907-0.0390.15420.0044-0.07490.03870.0425-0.0093-0.10450.00030.13640.0032-0.00910.2092-0.06930.2283-9.13813.4627-16.5538
20.2382-0.3544-0.32581.65490.72870.7779-0.063-0.07880.00040.0874-0.0685-0.0240.2240.00760.13150.26370.07470.01290.3276-0.02680.27438.9997-18.975-22.5688
37.32390.3868-2.57283.1027-0.50649.2821-0.1677-0.0122-0.2034-0.3508-0.20450.00950.05670.02420.37220.1625-0.00760.06080.184-0.02090.052611.69917.4075-49.8311
410.2871-7.4719-3.7619.57647.72754.70370.1537-0.1407-0.54850.55650.8979-0.4259-0.05880.7555-1.05160.2125-0.0629-0.08830.5045-0.18840.413910.50711.1625-29.4493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 455
2X-RAY DIFFRACTION2A456 - 795
3X-RAY DIFFRACTION3A796 - 922
4X-RAY DIFFRACTION4C1 - 10
5X-RAY DIFFRACTION4D1 - 10

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