9J6K | pdb_00009j6k

HBx complexed with DDB1

• PDB DOI: https://doi.org/10.2210/pdb9J6K/pdb
• EM Map EMD-61175: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Hepatitis B virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-16 Released: 2025-06-04 
• Deposition Author(s): Tanaka, H., Kita, S., Sasaki, M., Maenaka, K., Machida, S.
• Funding Organization(s): Other government, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of the hepatitis B virus X protein in complex with DDB1.

Tanaka, H., Diogo Dias, J., Jay, B., Kita, S., Sasaki, M., Takeda, H., Kishimoto, N., Sasaki, S., Misumi, S., Mizokami, M., Neuveut, C., Sumikama, T., Shibata, M., Maenaka, K., Machida, S.

(2025) Proc Natl Acad Sci U S A 122: e2421325122-e2421325122

• PubMed: 40512786 
• DOI: https://doi.org/10.1073/pnas.2421325122
• Primary Citation of Related Structures:  
  9J6J, 9J6K


• PubMed 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), 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.

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Organizational Affiliation: 
• Department of Structural Virology, National Institute of Global Health and Medicine, Japan Institute for Health Security, Shinjuku-ku, Tokyo 162-8655, Japan.
Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier, Montpellier 34000, France.
Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
Division of Proteo-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan.
Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan.
World Premier International Research Center Initiative, Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.
High-speed Atomic Force Microscopy for Biological Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.
Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan.
Hokkaido University Institute for Vaccine Research and Development, Sapporo 060-0812, Japan.
Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 145.81 kDa 
• Atom Count: 8,936 
• Modeled Residue Count: 1,141 
• Deposited Residue Count: 1,315 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	1,144	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein X	B	171	Hepatitis B virus	Mutation(s): 0
UniProt
Find proteins for Q77UW5 (Hepatitis B virus) Explore Q77UW5  Go to UniProtKB:  Q77UW5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Tanaka, H., Kita, S., Sasaki, M., Maenaka, K., Machida, S.

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Funding Organization	Location	Grant Number
Other government	Japan	22T003
Other government	Japan	23A1017
Japan Agency for Medical Research and Development (AMED)	Japan	JP20ae0101047
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121037
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627005

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Data collection, Database references