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- EMDB-66082: Calyx from human sperm -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-66082
TitleCalyx from human sperm
Map data
Sample
  • Cell: calyx
KeywordsCalyx arm / acrosome / human sperm / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 10.5 Å
AuthorsHe J / Wu J / Lei M
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structural Insights into Compartmentalization in Human Sperm
Authors: He J / Wu J / Lei M
History
DepositionSep 3, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66082.png

Downloads & links

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Map

FileDownload / File: emd_66082.map.gz / Format: CCP4 / Size: 10.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 142 pix.
= 340.8 Å		2.4 Å/pix.
x 142 pix.
= 340.8 Å		2.4 Å/pix.
x 142 pix.
= 340.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000626
Minimum - Maximum-0.0035915514 - 0.0035459278
Average (Standard dev.)0.000012516474 (±0.00014003029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions142142142
Spacing142142142
CellA=B=C: 340.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66082_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66082_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_66082_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 : calyx

EntireName: calyx
Components
  • Cell: calyx

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Supramolecule #1: calyx

SupramoleculeName: calyx / type: cell / ID: 1 / Parent: 0
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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 22884
ExtractionNumber tomograms: 66 / Number images used: 52932 / Software - Name: IMOD
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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