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- PDB-9flg: Solution NMR structure of the Delta60 domain of the hepatitis del... -

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Basic information

Entry
Database: PDB / ID: 9flg
TitleSolution NMR structure of the Delta60 domain of the hepatitis delta virus small antigen SHDAg
ComponentsLarge delta antigen
KeywordsVIRAL PROTEIN / Hepatitis Delta virus / HDV / delta60 / S-HDAg / RNA interaction
Function / homology
Function and homology information


virion component / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / RNA binding
Similarity search - Function
Hepatitis delta virus delta antigen / Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile.
Similarity search - Domain/homology
Biological speciesEscherichia coli BL21 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYang, Y. / Delcourte, L. / Fogeron, M.L. / Bockmann, A. / Lecoq, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ158948 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structure and nucleic acid interactions of the S Delta 60 domain of the hepatitis delta virus small antigen.
Authors: Yang, Y. / Delcourte, L. / van Belleghem, C. / Fonte, S. / Gerard, K. / Baconnais, S. / Callon, M. / Le Cam, E. / Fogeron, M.L. / Levrero, M. / Faivre-Moskalenko, C. / Bockmann, A. / Lecoq, L.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large delta antigen


Theoretical massNumber of molelcules
Total (without water)15,1501
Polymers15,1501
Non-polymers00
Water00
1


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

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Components

#1: Protein Large delta antigen


Mass: 15149.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residues 61-195 / Source: (natural) Escherichia coli BL21 (bacteria) / Variant: CodonPlus / References: UniProt: O39946
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 SOFAST
121isotropic13D 13C-NOESY-HSQC
131isotropic13D 15N-NOESY-HSQC
242isotropic23D B-HNCO
252isotropic23D BT-HN(CA)CO
262isotropic23D HN(CA)CB
272isotropic23D C(CO)NH
282isotropic23D H(CCO)NH
292isotropic22D HC-HSQC
2102isotropic23D (H)CCH-TOCSY
2112isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1160 uM [U-100% 13C; U-100% 15N] Delta60 domain of the hepatitis delta virus small antigen, 90% H2O/10% D2O13C-15N_sample190% H2O/10% D2O
solution2200 uM [U-100% 13C; U-100% 15N] Delta60 domain of the hepatitis delta virus small antigen, 90% H2O/10% D2O13C-15N_sample290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
160 uMDelta60 domain of the hepatitis delta virus small antigen[U-100% 13C; U-100% 15N]1
200 uMDelta60 domain of the hepatitis delta virus small antigen[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM NaCl mMCondition_16.71 atm298 K
250 mM NaCl mMCondition_26.51 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III9501IBS Grenoble, cryoprobe
Bruker AVANCE IIIBrukerAVANCE III6002CRMN Lyon, cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5CCPNchemical shift assignment
TopSpin4.3Brukercollection
ARIA2Linge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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