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- PDB-9j6j: HBx fused DDB1 4M mutant -

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Basic information

Entry
Database: PDB / ID: 9j6j
TitleHBx fused DDB1 4M mutant
ComponentsProtein X,DNA damage-binding protein 1
KeywordsVIRAL PROTEIN / HBV / complex
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 / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated arrest of host cell cycle during G2/M transition / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / host cell mitochondrion / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / viral genome replication / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA-templated transcription / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / host cell nucleus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transactivation protein X / Trans-activation protein X / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / Protein X
Similarity search - Component
Biological speciesHepatitis B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsTanaka, H. / Kita, S. / Sasaki, M. / Maenaka, K. / Machida, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Other government22T003 Japan
Other government23A1017 Japan
Japan Agency for Medical Research and Development (AMED)JP20ae0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627005 Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis of the hepatitis B virus X protein in complex with DDB1.
Authors: Hiroki Tanaka / Joao Diogo Dias / Basile Jay / Shunsuke Kita / Mina Sasaki / Hiroyuki Takeda / Naoki Kishimoto / Shunsuke Sasaki / Shogo Misumi / Masashi Mizokami / Christine Neuveut / ...Authors: Hiroki Tanaka / Joao Diogo Dias / Basile Jay / Shunsuke Kita / Mina Sasaki / Hiroyuki Takeda / Naoki Kishimoto / Shunsuke Sasaki / Shogo Misumi / Masashi Mizokami / Christine Neuveut / Takashi Sumikama / Mikihiro Shibata / Katsumi Maenaka / Shinichi Machida /
Abstract: A cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this approach is the hepatitis B virus (HBV) X protein (HBx), ...A cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this approach is the hepatitis B virus (HBV) X protein (HBx), which is a key factor that promotes transcription from cccDNA. However, the HBx structure remains unsolved. Here, we present the cryoelectron microscopy structure of HBx in complex with DDB1, which is an essential complex for cccDNA transcription. In this structure, hydrophobic interactions within HBx were identified, and mutational analysis highlighted their importance in the HBV life cycle. Our biochemical analysis revealed that the HBx-DDB1 complex directly interacts simultaneously with NSE3, which is a component of the SMC5/6 complex, and Spindlin1. Additionally, HBx-DDB1 complex dynamics were explored via high-speed atomic force microscopy. These findings provide comprehensive insights into the structure and function of HBx in HBV replication.
History
DepositionAug 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.2Jun 25, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein X,DNA damage-binding protein 1


Theoretical massNumber of molelcules
Total (without water)146,2581
Polymers146,2581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein X,DNA damage-binding protein 1 / HBx / Peptide X / pX / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA- ...HBx / Peptide X / pX / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 146258.094 Da / Num. of mol.: 1 / Mutation: A583D,W774K,I770D,R772E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus, (gene. exp.) Homo sapiens (human)
Gene: DDB1, XAP1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q77UW5, UniProt: Q16531
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: the complex of HBx and DDB1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Hepatitis B virus10407
Source (recombinant)Organism: Homo sapiens (human) / Strain: Expi293
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57281 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099138
ELECTRON MICROSCOPYf_angle_d0.92912377
ELECTRON MICROSCOPYf_dihedral_angle_d6.8341226
ELECTRON MICROSCOPYf_chiral_restr0.0561429
ELECTRON MICROSCOPYf_plane_restr0.0061594

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