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- PDB-2lwd: Solution structure of second CARD of human RIG-I -

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Basic information

Entry
Database: PDB / ID: 2lwd
TitleSolution structure of second CARD of human RIG-I
ComponentsProbable ATP-dependent RNA helicase DDX58
KeywordsSIGNALING PROTEIN / RIG-I / CARD / SENSOR / VIRAL RNA / HELICASE
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
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. / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain ...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. / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Death Domain, Fas / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Death-like domain superfamily / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDutta, K. / Ferrage, F. / Aggarwal, A.
CitationJournal: Structure / Year: 2012
Title: Structure and Dynamics of the Second CARD of Human RIG-I Provide Mechanistic Insights into Regulation of RIG-I Activation.
Authors: Ferrage, F. / Dutta, K. / Nistal-Villan, E. / Patel, J.R. / Sanchez-Aparicio, M.T. / De Ioannes, P. / Buku, A. / Aseguinolaza, G.G. / Garcia-Sastre, A. / Aggarwal, A.K.
History
DepositionJul 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58


Theoretical massNumber of molelcules
Total (without water)11,7831
Polymers11,7831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX58


Mass: 11782.896 Da / Num. of mol.: 1 / Fragment: CARD 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RPL / References: UniProt: O95786

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HN(CA)CB
1423D HCACO
1523D CBCA(CO)NH
1623D HBHA(CO)NH
1723D C(CO)NH
1823D H(CCO)NH
1923D 1H-15N NOESY
11033D 1H-13C NOESY aliphatic
11133D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-100% 15N] card2, 95% H2O/5% D2O95% H2O/5% D2O
2300 uM [U-100% 13C; U-100% 15N] card2, 95% H2O/5% D2O95% H2O/5% D2O
3300 uM [U-100% 13C; U-100% 15N] card2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMcard2-1[U-100% 15N]1
300 uMcard2-2[U-100% 13C; U-100% 15N]2
300 uMcard2-3[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 250 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance9002
Bruker AvanceBrukerAvance8003
Bruker AvanceBrukerAvance7004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgeschemical shift assignment
NMRView8.3Johnson, One Moon Scientificchemical shift assignment
NMRView8.3Johnson, One Moon Scientificchemical shift calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2646 / NOE intraresidue total count: 945 / NOE long range total count: 381 / NOE medium range total count: 128 / NOE sequential total count: 445
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2100 / Conformers submitted total number: 20

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