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- EMDB-65483: In situ Tspan-7 spiral structure in retraction fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-65483
TitleIn situ Tspan-7 spiral structure in retraction fiber
Map data
Sample
  • Organelle or cellular component: Tspan-7 spiral assembly in membrane tube
KeywordsMembrane curvature / cell protrusion / helical structure / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodhelical reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsJia X / Wang DJ / Li XP / Liu N / Yu L / Wang HW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Vita / Year: 2026
Title: Polymerization of tetraspanin 7 into helical transmembrane skeletons for
Authors: Wang D / Jia X / Dharan R / Ren J / Zheng Y / Li X / Huang M / Xu K / Zhang Q / Sho T / Liu S / Yang F / Zhang QC / Sorkin R / Liu N / Wang HW / Yu L
History
DepositionJul 22, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65483.png

Downloads & links

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Map

FileDownload / File: emd_65483.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.18321335 - 0.3711717
Average (Standard dev.)0.013201614 (±0.03554448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65483_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65483_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_65483_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 : Tspan-7 spiral assembly in membrane tube

EntireName: Tspan-7 spiral assembly in membrane tube
Components
  • Organelle or cellular component: Tspan-7 spiral assembly in membrane tube

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Supramolecule #1: Tspan-7 spiral assembly in membrane tube

SupramoleculeName: Tspan-7 spiral assembly in membrane tube / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 66.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 6.547 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105167
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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