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- PDB-8zu6: Solution NMR Structure of PACT D3 Homodimer -

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Entry
Database: PDB / ID: 8zu6
TitleSolution NMR Structure of PACT D3 Homodimer
ComponentsInterferon-inducible double-stranded RNA-dependent protein kinase activator A
KeywordsPROTEIN BINDING / dsRNA-binding protein
Function / homology
Function and homology information


regulation of regulatory ncRNA processing / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / RISC complex ...regulation of regulatory ncRNA processing / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / RISC complex / outer ear morphogenesis / skeletal system morphogenesis / middle ear morphogenesis / MicroRNA (miRNA) biogenesis / protein kinase activator activity / positive regulation of intrinsic apoptotic signaling pathway / antiviral innate immune response / enzyme activator activity / PKR-mediated signaling / response to virus / double-stranded RNA binding / cellular response to oxidative stress / protein stabilization / immune response / negative regulation of cell population proliferation / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
PRKRA, first double-stranded RNA binding domain / PRKRA, second double-stranded RNA binding domain / PRKRA, third double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Interferon-inducible double-stranded RNA-dependent protein kinase activator A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsZhao, L. / Ahmad, S. / Hur, S. / Chou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2025
Title: PACT prevents aberrant activation of PKR by endogenous dsRNA without sequestration.
Authors: Ahmad, S. / Zou, T. / Hwang, J. / Zhao, L. / Wang, X. / Davydenko, A. / Buchumenski, I. / Zhuang, P. / Fishbein, A.R. / Capcha-Rodriguez, D. / Orgel, A. / Levanon, E.Y. / Myong, S. / Chou, J. ...Authors: Ahmad, S. / Zou, T. / Hwang, J. / Zhao, L. / Wang, X. / Davydenko, A. / Buchumenski, I. / Zhuang, P. / Fishbein, A.R. / Capcha-Rodriguez, D. / Orgel, A. / Levanon, E.Y. / Myong, S. / Chou, J. / Meyerson, M. / Hur, S.
History
DepositionJun 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Interferon-inducible double-stranded RNA-dependent protein kinase activator A
B: Interferon-inducible double-stranded RNA-dependent protein kinase activator A


Theoretical massNumber of molelcules
Total (without water)20,5432
Polymers20,5432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-inducible double-stranded RNA-dependent protein kinase activator A / PKR-associated protein X / PKR-associating protein X / Protein activator of the interferon-induced ...PKR-associated protein X / PKR-associating protein X / Protein activator of the interferon-induced protein kinase / Protein kinase / interferon-inducible double-stranded RNA-dependent activator


Mass: 10271.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKRA, PACT, RAX, HSD-14, HSD14 / Production host: Escherichia coli (E. coli) / References: UniProt: O75569
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic22D 1H-1H NOESY
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D CBCA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-13C; U-15N] PACT D3, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution20.7 mM [U-15N] PACT D3, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMPACT D3[U-13C; U-15N]1
0.7 mMPACT D3[U-15N]2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.refinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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