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- PDB-2rqa: Solution structure of LGP2 CTD -

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Basic information

Entry
Database: PDB / ID: 2rqa
TitleSolution structure of LGP2 CTD
ComponentsATP-dependent RNA helicase DHX58
KeywordsHYDROLASE / RNA binding protein / ATP-binding / Coiled coil / Cytoplasm / Helicase / Immune response / Innate immunity / Nucleotide-binding / Polymorphism / RNA-binding
Function / homology
Function and homology information


positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / antiviral innate immune response / positive regulation of type I interferon production / negative regulation of innate immune response ...positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / antiviral innate immune response / positive regulation of type I interferon production / negative regulation of innate immune response / response to bacterium / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / RNA helicase / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / 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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit ...RIG-I-like receptor, C-terminal regulatory domain / 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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DHX58
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTakahasi, K. / Kumeta, H. / Tsuduki, N. / Narita, R. / Shigemoto, T. / Hirai, R. / Yoneyama, M. / Horiuchi, M. / Ogura, K. / Fujita, T. / Fuyuhiko, I.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Solution Structures of Cytosolic RNA Sensor MDA5 and LGP2 C-terminal Domains: IDENTIFICATION OF THE RNA RECOGNITION LOOP IN RIG-I-LIKE RECEPTORS
Authors: Takahasi, K. / Kumeta, H. / Tsuduki, N. / Narita, R. / Shigemoto, T. / Hirai, R. / Yoneyama, M. / Horiuchi, M. / Ogura, K. / Fujita, T. / Inagaki, F.
History
DepositionMar 17, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6182
Polymers15,5531
Non-polymers651
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 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP-dependent RNA helicase DHX58 / ATP-dependent helicase LGP2 / Protein D11Lgp2 homolog


Mass: 15553.013 Da / Num. of mol.: 1 / Fragment: UNP residues 546-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX58, D11LGP2E, LGP2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96C10, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D HNHA
11313D 1H-15N NOESY
11413D 1H-15N TOCSY
11513D HN(COCA)CB

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] LGP2, 50mM TRIS-2, 250mM sodium chloride-3, 1mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMLGP2[U-100% 13C; U-100% 15N]1
50 mMTRIS-21
250 mMsodium chloride-31
1 mMDTT-41
Sample conditionsIonic strength: 0.25 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
CYANAGuntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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