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- PDB-9ujo: Solution structure of MeV Vc 221-299 -

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Basic information

Entry
Database: PDB / ID: 9ujo
TitleSolution structure of MeV Vc 221-299
ComponentsNon-structural protein V
KeywordsVIRUS / STAT transcription factors / immune evasion / innate immunity / measles / paramyxovirus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / host cell cytoplasm / metal ion binding
Similarity search - Function
Paramyxovirinae protein V, zinc-binding domain / Zinc-binding domain of Paramyxoviridae V protein / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus
Similarity search - Domain/homology
Non-structural protein V
Similarity search - Component
Biological speciesMeasles morbillivirus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKumeta, H. / Ose, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01959 Japan
CitationJournal: To Be Published
Title: Mechanistic analysis of STAT2 targeting by measles virus V protein
Authors: Morita, K. / Goda, N. / Kimoto, M. / Inoue, I.S. / Yabuno, N. / Sugiyama, A. / Kumeta, H. / Ose, T.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3773
Polymers9,2471
Non-polymers1312
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Non-structural protein V


Mass: 9246.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Gene: P / Production host: Escherichia coli (E. coli) / References: UniProt: G4XDT3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-15N HMQC
131isotropic12D 1H-13C HSQC
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D CBCA(CO)NH
171isotropic13D HN(CA)CB
181isotropic13D C(CO)NH
191isotropic13D HBHA(CO)NH
1101isotropic13D 15N-separated NOESY
1111isotropic13D 13C-separated NOESY
1121isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 130 uM [U-99% 13C; U-99% 15N] MeV Vc, 1 mM TCEP, 10 mM HEPES, 100 % 96.2% H2O 3.8% D2O, 96.2% H2O 3.8% D2O
Label: sample_1 / Solvent system: 96.2% H2O 3.8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
130 uMMeV Vc[U-99% 13C; U-99% 15N]1
1 mMTCEPnatural abundance1
10 mMHEPESnatural abundance1
100 %96.2% H2O 3.8% D2Onatural abundance1
Sample conditionsIonic strength: 11 mM / Label: sample_conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.1.4Bruker Biospincollection
NMRPipe8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
TALOS+8.2Shen, Delaglio, Cornilescu, and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Sparky3.113Goddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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