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- EMDB-65519: in situ Tspan-7 spiral structure in cellular retraction fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-65519
Titlein situ Tspan-7 spiral structure in cellular retraction fiber
Map dataAuthor claim: The reconstruction corresponds to a sub-tomogram average (STA) of a continuous filamentous assembly generated prior to single-particle helical reconstruction and local refinement. Due to the intrinsic helical and axial continuity of the specimen, adjacent sub-tomograms are not statistically independent, even after particle picking with a 60 A step size that approximates the helical rise and includes intentional redundancy reduction along the filament axis. Under these conditions, the STA dataset contains inherent sampling overlap, and residual correlations at long spatial frequencies are therefore expected. As a result, the FSC curve does not decay to zero as observed in reconstructions based on independent particle sampling. This behavior is a known consequence of overlapping sampling in filamentous STA workflows and does not indicate overfitting. Importantly, this reconstruction is not used for final structural interpretation or model building. It serves strictly as an intermediate reference for downstream single-particle helical reconstruction and local refinement. No atomic model was built on this map, and no structural claims are derived from it. To avoid misinterpretation, we have clarified in the Methods that this represents a redundancy-inherent, non-independent STA intermediate generated from a continuous filamentous assembly, and we have omitted the associated resolution statement.
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: 16.0 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 24, 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_65519.png

Downloads & links

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Map

FileReleased
AnnotationAuthor claim: The reconstruction corresponds to a sub-tomogram average (STA) of a continuous filamentous assembly generated prior to single-particle helical reconstruction and local refinement. Due to the intrinsic helical and axial continuity of the specimen, adjacent sub-tomograms are not statistically independent, even after particle picking with a 60 A step size that approximates the helical rise and includes intentional redundancy reduction along the filament axis. Under these conditions, the STA dataset contains inherent sampling overlap, and residual correlations at long spatial frequencies are therefore expected. As a result, the FSC curve does not decay to zero as observed in reconstructions based on independent particle sampling. This behavior is a known consequence of overlapping sampling in filamentous STA workflows and does not indicate overfitting. Importantly, this reconstruction is not used for final structural interpretation or model building. It serves strictly as an intermediate reference for downstream single-particle helical reconstruction and local refinement. No atomic model was built on this map, and no structural claims are derived from it. To avoid misinterpretation, we have clarified in the Methods that this represents a redundancy-inherent, non-independent STA intermediate generated from a continuous filamentous assembly, and we have omitted the associated resolution statement.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 100 pix.
= 544. Å		5.44 Å/pix.
x 100 pix.
= 544. Å		5.44 Å/pix.
x 100 pix.
= 544. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.44 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.81
Minimum - Maximum-0.5912206 - 1.3393049
Average (Standard dev.)0.03845553 (±0.28973588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65519_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_65519_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_65519_half_map_2.map
Projections & Slices
AxesZYX

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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: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 3572
ExtractionNumber tomograms: 114 / Number images used: 11355 / Software - Name: Warp
CTF correctionType: NONE
Final angle assignmentType: NOT APPLICABLE

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