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- PDB-3tbk: Mouse RIG-I ATPase Domain -

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Basic information

Entry
Database: PDB / ID: 3tbk
TitleMouse RIG-I ATPase Domain
ComponentsRIG-I Helicase Domain
KeywordsHYDROLASE / DECH Helicase / Helicase / ATP binding
Function / homology
Function and homology information


OAS antiviral response / Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / detection of virus / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity ...OAS antiviral response / Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / detection of virus / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / 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 / bicellular tight junction / 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 / response to virus / ruffle membrane / positive regulation of interleukin-6 production / double-stranded RNA binding / actin cytoskeleton / positive regulation of tumor necrosis factor production / gene expression / double-stranded DNA binding / defense response to virus / single-stranded RNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / 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, 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsCivril, F. / Bennett, M.D. / Hopfner, K.-P.
CitationJournal: Embo Rep. / Year: 2011
Title: The RIG-I ATPase domain structure reveals insights into ATP-dependent antiviral signalling.
Authors: Civril, F. / Bennett, M. / Moldt, M. / Deimling, T. / Witte, G. / Schiesser, S. / Carell, T. / Hopfner, K.P.
History
DepositionAug 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIG-I Helicase Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0383
Polymers63,4701
Non-polymers5682
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.144, 86.027, 153.097
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 RIG-I Helicase Domain / 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: 63470.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddx58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q899, RNA helicase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.39 Å3/Da / Density % sol: 48.62 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 34468 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.14→2.27 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.autosolve)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→43.891 Å / SU ML: 0.62 / σ(F): 2.04 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1724 5 %RANDOM
Rwork0.1873 ---
obs0.1898 34468 99.53 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.285 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1779 Å20 Å20 Å2
2--0.4208 Å20 Å2
3---5.7571 Å2
Refinement stepCycle: LAST / Resolution: 2.14→43.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 35 306 4521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084284
X-RAY DIFFRACTIONf_angle_d1.0815782
X-RAY DIFFRACTIONf_dihedral_angle_d14.2341636
X-RAY DIFFRACTIONf_chiral_restr0.066662
X-RAY DIFFRACTIONf_plane_restr0.004734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.20060.27921350.20872566X-RAY DIFFRACTION95
2.2006-2.27160.21831410.18462673X-RAY DIFFRACTION100
2.2716-2.35280.25091410.1782688X-RAY DIFFRACTION100
2.3528-2.4470.26521440.1942726X-RAY DIFFRACTION100
2.447-2.55830.291420.20852693X-RAY DIFFRACTION100
2.5583-2.69320.30631430.2112720X-RAY DIFFRACTION100
2.6932-2.86190.28741430.20462719X-RAY DIFFRACTION100
2.8619-3.08280.26441440.19222741X-RAY DIFFRACTION100
3.0828-3.39290.2331430.18752716X-RAY DIFFRACTION100
3.3929-3.88360.22731460.17762771X-RAY DIFFRACTION100
3.8836-4.89190.15741470.16082790X-RAY DIFFRACTION100
4.8919-43.90.24991550.19582941X-RAY DIFFRACTION100

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