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- PDB-9vuy: NMR Structure of LC3B in complex with HBx BH3-like motif -

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Basic information

Entry
Database: PDB / ID: 9vuy
TitleNMR Structure of LC3B in complex with HBx BH3-like motif
Components
  • HBx BH3-like motif
  • Microtubule-associated protein 1 light chain 3 beta
KeywordsVIRAL PROTEIN / Complex / HBx / LC3B
Function / homology
Function and homology information


symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated arrest of host cell cycle during G2/M transition / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy ...symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated arrest of host cell cycle during G2/M transition / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane / autophagosome maturation / autophagosome assembly / axoneme / mitophagy / host cell mitochondrion / endomembrane system / autophagosome / viral genome replication / cellular response to starvation / Pexophagy / macroautophagy / PINK1-PRKN Mediated Mitophagy / Dengue Virus Genome Translation and Replication / mitochondrial membrane / autophagy / KEAP1-NFE2L2 pathway / cytoplasmic vesicle / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / microtubule / ubiquitin protein ligase binding / host cell nucleus / mitochondrion / DNA-templated transcription / cytosol
Similarity search - Function
Transactivation protein X / Trans-activation protein X / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein X / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / torsion angle dynamics
AuthorsKusunoki, H. / Nagata, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Other governmentJP22K06574 Japan
Other governmentJP25K09922 Japan
Other privateZE2024A-23 Japan
Other privateZE2025A-08 Japan
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2026
Title: Structural insights into the interaction between the BH3-like domain of hepatitis B virus X protein and LC3B.
Authors: Kusunoki, H. / Tanaka, T. / Mizukami, T. / Wakamatsu, K. / Nagata, T.
History
DepositionJul 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein 1 light chain 3 beta
B: HBx BH3-like motif


Theoretical massNumber of molelcules
Total (without water)15,7322
Polymers15,7322
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Microtubule-associated protein 1 light chain 3 beta / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / Microtubule-associated proteins 1A/1B light chain 3B / MAP1A/MAP1B LC3 B / MAP1A/MAP1B light chain 3 B


Mass: 14093.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Protein/peptide HBx BH3-like motif / HBx / Peptide X / pX


Mass: 1638.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein X / Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q913A9
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
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
1171isotropic13D HBHA(CO)NH
1161isotropic13D CC(CO)NH
1151isotropic13D 1H-15N NOESY-HSQC
1141isotropic12D 1H-13C HSQC aliphatic
1131isotropic13D (H)CCH-TOCSY aliphatic
1121isotropic13D CCH-TOCSY aliphatic
1111isotropic13D 1H-13C NOESY-HSQC aliphatic
1521isotropic12D 1H-13C HSQC aromatic
1511isotropic13D (H)CCH-COSY aromatic
1271isotropic13D 1H-13C NOESY-HSQC aromatic
1104isotropic12D 1H-15N HSQC
194isotropic13D 1H-15N NOESY-HSQC
185isotropic12D 1H-15N HSQC
175isotropic13D HNCO
165isotropic13D HNCA
1265isotropic13D CBCA(CO)NH
1255isotropic13D HBHA(CO)NH
1245isotropic13D CC(CO)NH
1235isotropic13D 1H-15N NOESY-HSQC
1225isotropic12D 1H-13C HSQC
1215isotropic13D (H)CCH-TOCSY
1205isotropic13D 1H-13C NOESY-HSQC aromatic
1195isotropic13D 1H-13C NOESY-HSQC
1185isotropic12D 13C,15N-[F1,F2]-filtered NOESY
1325isotropic12D 13C,15N-[F2]-filtered NOESY
1315isotropic12D 13C,15N-[F2]-filtered TOCSY
1305isotropic13D [F1] 13C-filtered [F3] 13C-edited NOESY-HSQC
1293isotropic12D 1H-15N HSQC
1283isotropic13D BEST-HNCO
1383isotropic13D BEST-HN(CA)CO
1373isotropic13D BEST-HNCA
1363isotropic13D BEST-HN(CO)CA
1353isotropic13D BEST-HN(CO)CACB
1343isotropic13D BEST-HN(CA)CB
1333isotropic13D HBHA(CO)NH
1433isotropic13D CC(CO)NH
1423isotropic13D 1H-15N NOESY-HSQC
1413isotropic13D HNHA
1403isotropic12D 1H-13C HSQC aliphatic
1393isotropic13D (H)CCH-TOCSY aliphatic
1473isotropic13D CCH-TOCSY aliphatic
1463isotropic13D 1H-13C NOESY-HSQC aliphatic
1453isotropic12D 1H-13C HSQC aromatic
1443isotropic13D (H)CCH-TOCSY aromatic
1503isotropic13D 1H-13C NOESY-HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-13C; U-15N] LC3B, 0.5 mM [U-13C; U-15N] HBx BH3-like motif, 95% H2O/5% D2O13C15N_LC3B_13C15N_HBx95% H2O/5% D2O
solution40.4 mM [U-15N] LC3B, 0.5 mM [U-15N] HBx BH3-like motif, 95% H2O/5% D2O15N_LC3B_15N_HBx95% H2O/5% D2O
solution30.8 mM 1H LC3B, 0.4 mM [U-13, U-15N] HBx BH3-like motif, 95% H2O/5% D2OLC3B_13C15N_HBx95% H2O/5% D2O
solution50.5 mM [U-13, U-15N] LC3B, 0.625 mM 1H HBx BH3-like motif, 95% H2O/5% D2O13C15N_LC3B_HBx95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMLC3B[U-13C; U-15N]1
0.5 mMHBx BH3-like motif[U-13C; U-15N]1
0.4 mMLC3B[U-15N]4
0.5 mMHBx BH3-like motif[U-15N]4
0.8 mMLC3B1H3
0.4 mMHBx BH3-like motif[U-13, U-15N]3
0.5 mMLC3B[U-13, U-15N]5
0.625 mMHBx BH3-like motif1H5
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMRV. Orekhov, V. Jaravine, M. Mayzel, and K. Kazimierczukprocessing
MagRO-NMRViewNaohiro, Kobayashidata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing3
torsion angle dynamics4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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