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- EMDB-65524: in situ Tspan7-GFP spiral in retraction fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-65524
Titlein situ Tspan7-GFP spiral in retraction fiber
Map dataAuthor claim: The FSC was calculated from two independently refined half-maps generated from a sub-tomogram averaging (STA) workflow of a continuous filamentous assembly. Due to the intrinsic helical axial continuity of the specimen, the sub-tomograms used for refinement are not fully statistically independent even after applying a 60 A step size along the filament axis, which approximately matches the helical rise and includes redundancy reduction. As a consequence, residual correlations at intermediate and long spatial frequencies are expected, and the FSC curve may plateau above zero rather than fully decaying. This behavior is a known outcome of redundancy-inherent STA sampling of continuous filamentous systems and does not indicate cross-contamination between the two half-sets or overfitting. The two half-maps were generated using standard independent half-set refinement procedures. Importantly, this reconstruction is not used for final structural interpretation or atomic model building and is only an intermediate map used to guide downstream engineered construction.
Sample
  • Cell: in situ Tspan-7 spiral in cellular retraction fibers
KeywordsMembrane curvature / cell protrusion / helical structure / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 22.0 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 25, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65524.png

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Map

FileReleased
AnnotationAuthor claim: The FSC was calculated from two independently refined half-maps generated from a sub-tomogram averaging (STA) workflow of a continuous filamentous assembly. Due to the intrinsic helical axial continuity of the specimen, the sub-tomograms used for refinement are not fully statistically independent even after applying a 60 A step size along the filament axis, which approximately matches the helical rise and includes redundancy reduction. As a consequence, residual correlations at intermediate and long spatial frequencies are expected, and the FSC curve may plateau above zero rather than fully decaying. This behavior is a known outcome of redundancy-inherent STA sampling of continuous filamentous systems and does not indicate cross-contamination between the two half-sets or overfitting. The two half-maps were generated using standard independent half-set refinement procedures. Importantly, this reconstruction is not used for final structural interpretation or atomic model building and is only an intermediate map used to guide downstream engineered construction.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 128 pix.
= 696.32 Å		5.44 Å/pix.
x 128 pix.
= 696.32 Å		5.44 Å/pix.
x 128 pix.
= 696.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.328
Minimum - Maximum-0.39124343 - 0.6909593
Average (Standard dev.)0.030911455 (±0.15830489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 696.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65524_msk_1.map
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Half map: #1

Fileemd_65524_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_65524_half_map_2.map
Projections & Slices
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Sample components

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Entire : in situ Tspan-7 spiral in cellular retraction fibers

EntireName: in situ Tspan-7 spiral in cellular retraction fibers
Components
  • Cell: in situ Tspan-7 spiral in cellular retraction fibers

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Supramolecule #1: in situ Tspan-7 spiral in cellular retraction fibers

SupramoleculeName: in situ Tspan-7 spiral in cellular retraction fibers / type: cell / 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
Processingsubtomogram averaging
Aggregation statecell

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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: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 4.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 3675
ExtractionNumber tomograms: 103 / Number images used: 9710 / Software - Name: Warp
CTF correctionType: NONE
Final angle assignmentType: NOT APPLICABLE

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