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- EMDB-65485: Tspan-7 dimer structure in retraction fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-65485
TitleTspan-7 dimer structure in retraction fiber
Map dataAuthor claim: Regarding the FSC curve, we carefully re-examined the refinement and the two independent half maps. We did not find evidence of half-set contamination during refinement. In our case, the reconstruction was performed using helical local refinement of the minimal repeat unit. For this type of reconstruction, the calculated FSC may remain slightly above zero at high spatial frequencies due to the combination of helical symmetry, local refinement, masking, and interpolation procedures, rather than indicating correlation introduced by mixing the two half datasets. The FSC crosses the 0.143 criterion at 6.63 A as expected, and the residual correlation at higher frequencies remains very low (approximately 0.02-0.03) without any abnormal increase, which we believe is consistent with residual background correlation rather than half-map contamination. We have carefully verified that the refinement followed gold-standard procedures using independent half datasets throughout the reconstruction.
Sample
  • Organelle or cellular component: Tspan-7 Dimer in Membrane Tube
KeywordsMembrane curvature / cell protrusion / MEMBRANE PROTEIN
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / Cell surface interactions at the vascular wall / plasma membrane
Similarity search - Function
: / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.87 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 23, 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_65485.png

Downloads & links

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Map

FileReleased
AnnotationAuthor claim: Regarding the FSC curve, we carefully re-examined the refinement and the two independent half maps. We did not find evidence of half-set contamination during refinement. In our case, the reconstruction was performed using helical local refinement of the minimal repeat unit. For this type of reconstruction, the calculated FSC may remain slightly above zero at high spatial frequencies due to the combination of helical symmetry, local refinement, masking, and interpolation procedures, rather than indicating correlation introduced by mixing the two half datasets. The FSC crosses the 0.143 criterion at 6.63 A as expected, and the residual correlation at higher frequencies remains very low (approximately 0.02-0.03) without any abnormal increase, which we believe is consistent with residual background correlation rather than half-map contamination. We have carefully verified that the refinement followed gold-standard procedures using independent half datasets throughout the reconstruction.
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: 0.561
Minimum - Maximum-5.7934704 - 7.7196956
Average (Standard dev.)0.017089449 (±0.06839119)
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_65485_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65485_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_65485_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 : Tspan-7 Dimer in Membrane Tube

EntireName: Tspan-7 Dimer in Membrane Tube
Components
  • Organelle or cellular component: Tspan-7 Dimer in Membrane Tube

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Supramolecule #1: Tspan-7 Dimer in Membrane Tube

SupramoleculeName: Tspan-7 Dimer 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
Processingsingle particle reconstruction
Aggregation stateparticle

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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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1472338
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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