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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: Proc Natl Acad Sci U S A / Year: 2026
Title: SUN5 forms a regular protein lattice reinforcing the sperm head-tail junction.
Authors: Jonas Moecking / Svetlana Doroshev / Miguel Ricardo Leung / Tzviya Zeev-Ben-Mordehai /
Abstract: Spermatozoa strongly rely on their streamlined morphology to successfully fertilize an oocyte. A striking example of a morphological defect resulting in infertility is acephalic spermatozoa syndrome, ...Spermatozoa strongly rely on their streamlined morphology to successfully fertilize an oocyte. A striking example of a morphological defect resulting in infertility is acephalic spermatozoa syndrome, a rare but severe condition leading to detachment of the sperm head and tail. Among the most common genetic causes for this syndrome are mutations in the linker of nucleo- and cytoskeleton (LINC) complex component SUN5. LINC complexes typically reside in the nuclear envelope, the double-membrane surrounding the nucleus, where they establish a physical bridge between nucleus and cytoplasm. This localization allows them to transduce mechanical signals from the cytoplasm to the nucleus and to regulate nuclear morphology. In sperm, LINC complexes are essential for a multitude of morphological changes during sperm development, including the reshaping of the nucleus and establishing a stable head-tail junction. Here, using superresolution fluorescence microscopy, we find that sperm-specific SUN5 localizes to the base of the head in human, mouse, and boar sperm. By applying in situ cryoelectron tomography, we find an extensive hexagonal lattice in the nuclear envelope in this region. This lattice appears to maintain a consistent close apposition between the inner and outer nuclear membranes (ONM). Further structural analysis supports a model in which LINC complexes form this lattice by laterally interacting at the ONM. Overall, this study sheds light on nuclear envelope organization in the highly streamlined sperm cell, providing a structural basis for uniform nuclear envelope spacing maintained by a LINC lattice and rationalizing the disruptive effects of SUN5 mutations.
History
DepositionDec 17, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 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
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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

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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
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Half map: half2

Fileemd_56104_half_map_1.map
Annotationhalf2
Projections & Slices
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Histogram

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Half map: half1

Fileemd_56104_half_map_2.map
Annotationhalf1
Projections & Slices
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Histogram

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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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