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- EMDB-56104: A LINC complex lattice in the nuclear envelope of ejaculated huma... -

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Basic information

Entry
Database: EMDB / ID: EMD-56104
TitleA LINC complex lattice in the nuclear envelope of ejaculated human sperm
Map datafull map
Sample
  • Cell: Human ejaculated sperm cells.
KeywordsLINC complex / 2D-lattice / sperm / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 13.7 Å
AuthorsMoecking J / Zeev-Ben-Mordhai T
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101088673European Union
H2020 Marie Curie Actions of the European Commission101153233European Union
CitationJournal: To Be Published
Title: SUN5 forms a regular protein lattice reinforcing the sperm head-tail junction
Authors: Moecking J / Zeev-Ben-Mordhai T
History
DepositionDec 17, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56104.png

Downloads & links

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Map

FileDownload / File: emd_56104.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.34 Å/pix.
x 180 pix.
= 781.2 Å		4.34 Å/pix.
x 180 pix.
= 781.2 Å		4.34 Å/pix.
x 180 pix.
= 781.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068
Minimum - Maximum-0.89590585 - 0.9401213
Average (Standard dev.)0.009520901 (±0.084200606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 781.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_56104_half_map_1.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_56104_half_map_2.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ejaculated sperm cells.

EntireName: Human ejaculated sperm cells.
Components
  • Cell: Human ejaculated sperm cells.

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Supramolecule #1: Human ejaculated sperm cells.

SupramoleculeName: Human ejaculated sperm cells. / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 296.15 K / Instrument: LEICA EM GP
DetailsEjaculated sperm was received fresh or frozen.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 13.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number subtomograms used: 15488
ExtractionNumber tomograms: 44 / Number images used: 28361 / Method: Surface model / Software - Name: RELION (ver. 5.0.0)
Details: The outer nuclear membrane was defined as a surface and particles were seeded using Dynamo. Particle coordinates were then transferred to Relion 5.0
CTF correctionSoftware - Name: RELION (ver. 5.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
FSC plot (resolution estimation)

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