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- PDB-6gpg: Structure of the RIG-I Singleton-Merten syndrome variant C268F -

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Basic information

Entry
Database: PDB / ID: 6gpg
TitleStructure of the RIG-I Singleton-Merten syndrome variant C268F
Components
  • Probable ATP-dependent RNA helicase DDX58
  • RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')
KeywordsANTIVIRAL PROTEIN / innate immune system / RIG-I / Singleton-Merten syndrome / RNA-dependent ATPase / RNA binding protein
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 / RSV-host interactions / cellular response to exogenous dsRNA / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / antiviral innate immune response / bicellular tight junction / positive regulation of interferon-alpha production / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / 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 / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.894 Å
AuthorsLaessig, C. / Lammens, K. / Hopfner, K.-P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationHO2489/8 Germany
German Research FoundationCRC1054 project B02 Germany
CitationJournal: Elife / Year: 2018
Title: Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants.
Authors: Lassig, C. / Lammens, K. / Gorenflos Lopez, J.L. / Michalski, S. / Fettscher, O. / Hopfner, K.P.
History
DepositionJun 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')
C: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')
A: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9425
Polymers90,8523
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-45 kcal/mol
Surface area34070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.620, 175.620, 109.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')


Mass: 4477.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 81896.367 Da / Num. of mol.: 1 / Mutation: C268F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95786, RNA helicase
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M MOPS pH 7.5, 17.5 % (w/v) PEG 3350, 0.25 M NaSCN, 3 % (v/v) 2,2,2 trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.894→46.468 Å / Num. obs: 22649 / % possible obs: 99.7 % / Redundancy: 13.09 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.72
Reflection shellResolution: 2.894→3 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.894→46.468 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68
RfactorNum. reflection% reflection
Rfree0.2597 1110 4.9 %
Rwork0.2096 --
obs0.2121 22649 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.894→46.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5258 552 2 0 5812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095988
X-RAY DIFFRACTIONf_angle_d1.2388198
X-RAY DIFFRACTIONf_dihedral_angle_d9.3883590
X-RAY DIFFRACTIONf_chiral_restr0.062930
X-RAY DIFFRACTIONf_plane_restr0.007954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.894-3.02570.40771420.34262588X-RAY DIFFRACTION98
3.0257-3.18520.35961210.3172658X-RAY DIFFRACTION100
3.1852-3.38470.34451470.28132637X-RAY DIFFRACTION100
3.3847-3.6460.35121400.24492665X-RAY DIFFRACTION100
3.646-4.01270.29751600.21212651X-RAY DIFFRACTION100
4.0127-4.59290.251350.18762695X-RAY DIFFRACTION100
4.5929-5.78480.23981060.20232761X-RAY DIFFRACTION100
5.7848-46.47420.21841590.18722884X-RAY DIFFRACTION100
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)
11.8463-0.11731.11192.76630.30312.734-0.28580.04710.7504-0.0718-0.0626-1.1794-0.45252.07510.57780.827-0.0642-0.1531.80220.43561.3146-92.180592.8558-7.7354
22.0002-0.05151.39141.9616-0.47541.45480.06070.30570.58060.0420.41030.4925-0.03411.14280.52170.8417-0.04-0.23811.69750.06771.0498-94.138990.4847-5.0042
31.8414-0.22090.63561.5123-0.11592.3802-0.2243-0.10660.45170.0734-0.1849-0.5205-0.30840.83550.34870.70610.11-0.10851.26430.13390.8867-100.060487.8819-0.5778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' )
2X-RAY DIFFRACTION2(chain 'C' )
3X-RAY DIFFRACTION3(chain 'I' )

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