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- EMDB-63366: HBx R96E fused DDB1 4M mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-63366
TitleHBx R96E fused DDB1 4M mutant
Map data
Sample
  • Complex: the complex of HBx and DDB1
    • Protein or peptide: Protein X, DNA damage-binding protein 1
KeywordsHBV / complex / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsTanaka H / Kita S / Sasaki M / Maenaka K / Machida S
Funding support Japan, 5 items
OrganizationGrant numberCountry
Other government22T003
Other government23A1017
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
DepositionFeb 5, 2025-
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_63366.png

Downloads & links

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Map

FileDownload / File: emd_63366.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0023
Minimum - Maximum-0.0055550183 - 0.011990441
Average (Standard dev.)0.000026743206 (±0.00036210415)
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: #1

Fileemd_63366_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63366_half_map_2.map
Projections & Slices
AxesZYX

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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: Protein X, DNA damage-binding protein 1

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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: Protein X, DNA damage-binding protein 1

MacromoleculeName: Protein X, DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAWSHPQF EKGSGSGMAA RLYCQLDPSR DVLCLRPVGA ESRGRPLSGP LGTLSSPSPS AVPADHGAHL SLRGLPVCAF SSAGPCALRF TSARCMETTV NAHQILPKVL HKETLGLPAM STTDLEAYFK DCVFKDWEEL GEEIRLKVFV LGGCRHKLVC APAPCNFFTS ...String:
MASAWSHPQF EKGSGSGMAA RLYCQLDPSR DVLCLRPVGA ESRGRPLSGP LGTLSSPSPS AVPADHGAHL SLRGLPVCAF SSAGPCALRF TSARCMETTV NAHQILPKVL HKETLGLPAM STTDLEAYFK DCVFKDWEEL GEEIRLKVFV LGGCRHKLVC APAPCNFFTS ASGSGSGSGS GSGMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNAC ILEYKQSGES IDIITRAHGN VQDRIGRPSE TGIIGIIDPE CRMIGLRLYD GLFKVIPLDR DNKELKAFNI RLEELHVIDV KFLYGCQAPT ICFVYQDPQG RHVKTYEVSL REKEFNKGPW KQENVEAEAS MVIAVPEPFG GAIIIGQESI TYHNGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNGVVFVGSR LGDSQLVKLN VDSNEQGSYV VAMETFTNLG PIVDMCVVDL ERQGQGQLVT CSGAFKEGSL RIIRNGIGIH EHDSIDLPGI KGLWPLRSDP NRETDDTLVL SFVGQTRVLM LNGEEVEETE LMGFVDDQQT FFCGNVAHQQ LIQITSASVR LVSQEPKALV SEWKEPQAKN ISVASCNSSQ VVVAVGRALY YLQIHPQELR QISHTEMEHE VACLDITPLG DSNGLSPLCA IGLKTDISAR ILKLPSFELL HKEMLGGEID PESILMTTFE SSHYLLCALG DGALFYFGLN IETGLLSDRK KVTLGTQPTV LRTFRSLSTT NVFACSDRPT VIYSSNHKLV FSNVNLKEVN YMCPLNSDGY PDSLALANNS TLTIGTIDEI QKLHIRTVPL YESPRKICYQ EVSQCFGVLS SRIEVQDTSG GTTALRPSAS TQALSSSVSS SKLFSSSTAP HETSFGEEVE VHNLLIIDQH TFEVLHAHQF LQNEYALSLV SCKLGKDPNT YFIVGTAMVY PEEAEPKQGR IVVFQYSDGK LQTVAEKEVK GAVYSMVEFN GKLLASINST VRLYEWTTEK ELRTECNHYN NIMALYLKTK GDFILVGDLM RSVLLLAYKP MEGNFEEIAR DFNPNWMSAV EILDDDNFLG AENAFNLFVC QKDSAATTDE ERQHLQEVGL FHLGEFVNVF CHGSLVMQNL GETSTPTQGS VLFGTVNGMI GLVTSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGMKREATAD DLIKVVEELT RIH

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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
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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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: 49.6 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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91049
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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