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- PDB-6bzh: Structure of mouse RIG-I tandem CARDs -

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Basic information

Entry
Database: PDB / ID: 6bzh
TitleStructure of mouse RIG-I tandem CARDs
ComponentsProbable ATP-dependent RNA helicase DDX58
KeywordsHYDROLASE / CARD RIG-I DEAD-box RNA Helicases
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 / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / antiviral innate immune response / bicellular tight junction / positive regulation of interferon-alpha production / positive regulation of defense response to virus by host / regulation of cell migration / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / response to virus / ruffle membrane / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / actin cytoskeleton / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / 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 / cytoplasm / cytosol
Similarity search - Function
RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / 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 ...RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKershaw, N.J. / D'Cruz, A.A. / Babon, J.J. / Nicholson, S.E.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Heath and Medical Research Council Australia
CitationJournal: Biochem. J. / Year: 2018
Title: Identification of a second binding site on the TRIM25 B30.2 domain.
Authors: D'Cruz, A.A. / Kershaw, N.J. / Hayman, T.J. / Linossi, E.M. / Chiang, J.J. / Wang, M.K. / Dagley, L.F. / Kolesnik, T.B. / Zhang, J.G. / Masters, S.L. / Griffin, M.D.W. / Gack, M.U. / Murphy, ...Authors: D'Cruz, A.A. / Kershaw, N.J. / Hayman, T.J. / Linossi, E.M. / Chiang, J.J. / Wang, M.K. / Dagley, L.F. / Kolesnik, T.B. / Zhang, J.G. / Masters, S.L. / Griffin, M.D.W. / Gack, M.U. / Murphy, J.M. / Nicola, N.A. / Babon, J.J. / Nicholson, S.E.
History
DepositionDec 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
E: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94812
Polymers113,5945
Non-polymers3557
Water61334
1
A: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,23011
Polymers90,8754
Non-polymers3557
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-34 kcal/mol
Surface area32830 Å2
2
E: Probable ATP-dependent RNA helicase DDX58


Theoretical massNumber of molelcules
Total (without water)22,7191
Polymers22,7191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area10290 Å2
Unit cell
Length a, b, c (Å)90.190, 97.560, 113.290
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 / 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: 22718.746 Da / Num. of mol.: 5
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate 26% w/v polyethylene glycol 3350 0.1 M Bis-Tris, pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95371 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 2.5→73.926 Å / Num. obs: 35016 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.06 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1824 / Net I/σ(I): 8.73
Reflection shellResolution: 2.5→2.589 Å / Mean I/σ(I) obs: 1.84 / CC1/2: 0.466 / Rrim(I) all: 1.379

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A2Q

4a2q


Resolution: 2.5→73.926 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1970 5.63 %
Rwork0.226 --
obs0.2289 35014 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→73.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 19 34 7688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027793
X-RAY DIFFRACTIONf_angle_d0.50110521
X-RAY DIFFRACTIONf_dihedral_angle_d12.1074747
X-RAY DIFFRACTIONf_chiral_restr0.0391143
X-RAY DIFFRACTIONf_plane_restr0.0031361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56260.33561360.30752226X-RAY DIFFRACTION96
2.5626-2.63190.37541420.3262340X-RAY DIFFRACTION100
2.6319-2.70930.38461270.31052353X-RAY DIFFRACTION100
2.7093-2.79680.37371400.29292324X-RAY DIFFRACTION100
2.7968-2.89670.33051490.28732349X-RAY DIFFRACTION100
2.8967-3.01270.32381370.25742355X-RAY DIFFRACTION100
3.0127-3.14980.31811330.25682357X-RAY DIFFRACTION100
3.1498-3.31590.30731420.24922343X-RAY DIFFRACTION100
3.3159-3.52360.29491400.22512359X-RAY DIFFRACTION100
3.5236-3.79570.27791460.20682377X-RAY DIFFRACTION100
3.7957-4.17760.20921480.1822358X-RAY DIFFRACTION99
4.1776-4.7820.21971240.16632415X-RAY DIFFRACTION100
4.782-6.02450.23061460.1962413X-RAY DIFFRACTION99
6.0245-73.95870.23231600.20172475X-RAY DIFFRACTION98

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