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- EMDB-65171: Cryo-ET structure of actin branch junction from B16F10 cells. -

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Basic information

Entry
Database: EMDB / ID: EMD-65171
TitleCryo-ET structure of actin branch junction from B16F10 cells.
Map dataCryo-ET map of actin branch junction from B16F10 cells.
Sample
  • Cell: In situ Arp2/3 branch junction.
KeywordsArp2-3 complex / Branch junctions / Cell migration / Cancer / CELL INVASION
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsWang ZY / Zhu Y / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Deciphering Arpin's In-Place Inhibitory Mode on Arp2/3-Mediated Actin Branching in Migrating Cells.
Authors: Wang ZY / Zhu Y / Sun F
History
DepositionJun 26, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65171.png

Downloads & links

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Map

FileDownload / File: emd_65171.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET map of actin branch junction from B16F10 cells.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.777
Minimum - Maximum-0.4615327 - 1.8675541
Average (Standard dev.)0.0061219353 (±0.15455502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65171_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET half map of actin branch junction from B16F10 cells.

Fileemd_65171_half_map_1.map
AnnotationCryo-ET half map of actin branch junction from B16F10 cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET half map of actin branch junction from B16F10 cells.

Fileemd_65171_half_map_2.map
AnnotationCryo-ET half map of actin branch junction from B16F10 cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ Arp2/3 branch junction.

EntireName: In situ Arp2/3 branch junction.
Components
  • Cell: In situ Arp2/3 branch junction.

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Supramolecule #1: In situ Arp2/3 branch junction.

SupramoleculeName: In situ Arp2/3 branch junction. / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 98 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 180.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 758
ExtractionNumber tomograms: 173 / Number images used: 758 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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