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- EMDB-63485: The consensus map of HBx-Smc5/6 ubiquitination complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63485
TitleThe consensus map of HBx-Smc5/6 ubiquitination complex
Map data
Sample
  • Complex: The consensus map of HBx-Smc5/6 ubiquitination complex
KeywordsHBx / Smc5/6 / Cul4A-RBx / HBV / ANTIVIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.84 Å
AuthorsTong C / Lili D / Hongshuai L / Jinhong Z / Qian X / Lanfeng W
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303600 China
CitationJournal: Cell Res / Year: 2026
Title: Structural and functional insights into HBx-Smc6 targeting for HBV inhibition.
Authors: Tong Cheng / Jinhong Zhou / Wenjun Huang / Lili Du / Pengyu He / Renzheng Yang / Yan Gao / Menghan Hao / Kongying Hu / Jieliang Chen / Hongxia Wang / Zihe Rao / Zhenghong Yuan / Lanfeng Wang /
History
DepositionFeb 18, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63485.png

Downloads & links

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Map

FileDownload / File: emd_63485.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.86 Å/pix.
x 560 pix.
= 1043.84 Å		1.86 Å/pix.
x 560 pix.
= 1043.84 Å		1.86 Å/pix.
x 560 pix.
= 1043.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.864 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.7975612 - 3.9900556
Average (Standard dev.)-0.0010138289 (±0.061336108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 1043.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63485_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63485_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_63485_half_map_2.map
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 consensus map of HBx-Smc5/6 ubiquitination complex

EntireName: The consensus map of HBx-Smc5/6 ubiquitination complex
Components
  • Complex: The consensus map of HBx-Smc5/6 ubiquitination complex

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Supramolecule #1: The consensus map of HBx-Smc5/6 ubiquitination complex

SupramoleculeName: The consensus map of HBx-Smc5/6 ubiquitination complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69510
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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