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- EMDB-61175: HBx complexed with DDB1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61175
TitleHBx complexed with DDB1
Map data
Sample
  • Complex: the complex of HBx and DDB1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein X
KeywordsHBV / complex / VIRAL PROTEIN
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 / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...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 / Cul4-RING E3 ubiquitin ligase complex / 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 / 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 / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / nucleotide-excision repair / 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 / regulation of circadian rhythm / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Wnt signaling pathway / 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 / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 speciesHomo sapiens (human) / Hepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsTanaka H / Kita S / Sasaki M / Maenaka K / Machida S
Funding support Japan, 5 items
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, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61175.png

Downloads & links

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Map

FileDownload / File: emd_61175.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 320 pix.
= 214.4 Å		0.67 Å/pix.
x 320 pix.
= 214.4 Å		0.67 Å/pix.
x 320 pix.
= 214.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0076904665 - 0.015522168
Average (Standard dev.)0.000038972954 (±0.0004110949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 214.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap 1

Fileemd_61175_half_map_1.map
Annotationhalfmap_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 2

Fileemd_61175_half_map_2.map
Annotationhalfmap_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the complex of HBx and DDB1

EntireName: the complex of HBx and DDB1
Components
  • Complex: the complex of HBx and DDB1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein X

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Supramolecule #1: the complex of HBx and DDB1

SupramoleculeName: the complex of HBx and DDB1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.457891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVMEL FRPKGESKDL LFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL YDGLFKVIPL DRDNKELKAF N IRLEELHV ...String:
MASAMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVMEL FRPKGESKDL LFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL YDGLFKVIPL DRDNKELKAF N IRLEELHV IDVKFLYGCQ APTICFVYQD PQGRHVKTYE VSLREKEFNK GPWKQENVEA EASMVIAVPE PFGGAIIIGQ ES ITYHNGD KYLAIAPPII KQSTIVCHNR VDPNGSRYLL GDMEGRLFML LLEKEEQMDG TVTLKDLRVE LLGETSIAEC LTY LDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLVTCSGAF KEGSLRIIRN GIGI HEHAS IDLPGIKGLW PLRSDPNRET DDTLVLSFVG QTRVLMLNGE EVEETELMGF VDDQQTFFCG NVAHQQLIQI TSASV RLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN GLSPLC AIG LWTDISARIL KLPSFELLHK EMLGGEIIPR SILMTTFESS HYLLCALGDG ALFYFGLNIE TGLLSDRKKV TLGTQPT VL RTFRSLSTTN VFACSDRPTV IYSSNHKLVF SNVNLKEVNY MCPLNSDGYP DSLALANNST LTIGTIDEIQ KLHIRTVP L YESPRKICYQ EVSQCFGVLS SRIEVQDTSG GTTALRPSAS TQALSSSVSS SKLFSSSTAP HETSFGEEVE VHNLLIIDQ HTFEVLHAHQ FLQNEYALSL VSCKLGKDPN TYFIVGTAMV YPEEAEPKQG RIVVFQYSDG KLQTVAEKEV KGAVYSMVEF NGKLLASIN STVRLYEWTT EKELRTECNH YNNIMALYLK TKGDFILVGD LMRSVLLLAY KPMEGNFEEI ARDFNPNWMS A VEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QNLGETSTPT QGSVLFGTVN GM IGLVTSL SESWYNLLLD MQNRLNKVIK SVGKIEHSFW RSFHTERKTE PATGFIDGDL IESFLDISRP KMQEVVANLQ YDD GSGMKR EATADDLIKV VEELTRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: Protein X

MacromoleculeName: Protein X / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 18.353215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASAWSHPQF EKGSGSGMAA RLYCQLDPSR DVLCLRPVGA ESRGRPLSGP LGTLSSPSPS AVPADHGAHL SLRGLPVCAF SSAGPCALR FTSARCMETT VNAHQILPKV LHKRTLGLPA MSTTDLEAYF KDCVFKDWEE LGEEIRLKVF VLGGCRHKLV C APAPCNFF TSA

UniProtKB: Protein X

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2b5m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1368931
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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