[English] 日本語
Yorodumi
- EMDB-64625: Cryo-EM structure of the 48-nm repeat doublet microtubule from Ts... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64625
TitleCryo-EM structure of the 48-nm repeat doublet microtubule from Tssk6 KO mouse sperm
Map data
Sample
  • Complex: sperm flagellar doublet microtubules
Keywordssperm flagellar doublet microtubules TSSK6 / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLiu Q / Gui M / Zhou LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: Doublet microtubule-associated tektins and enzymes differentially regulate sperm flagellar integrity and motility.
Authors: Qi Liu / Lunni Zhou / Xiaochen Liang / Pengyu Chen / Bo Li / Shuo Yang / Yuqi Liu / Haibo Zhao / Jin Hu / Shan Feng / Shanshan Xie / Jianping Wu / Miao Gui /
Abstract: Doublet microtubule (DMT)-associated proteins assemble and drive sperm flagella, which are essential for successful fertilization. However, the exact roles of different DMT-associated proteins in ...Doublet microtubule (DMT)-associated proteins assemble and drive sperm flagella, which are essential for successful fertilization. However, the exact roles of different DMT-associated proteins in sperm function and the underlying molecular mechanisms remain elusive. Here, we generate four gene-knockout mice based on high-resolution structures targeting distinct DMT components: two intermediate filament-like tektins (TEKT1, TEKT5) and two enzymes (TSSK6, DUSP21). The depletion of TEKT1, shared by sperm flagella and motile cilia, causes male infertility characterized by impaired sperm motility and loss of the tektin bundle, whereas sperm-specific Tekt5 knockout (KO) mice remain fertile with largely normal flagellar function, indicating functional divergence within the tektin family. Tssk6 KO spermatozoa exhibit severely disturbed morphology and motility, resulting in homozygote infertility and heterozygote subfertility. Phosphoproteomics reveals dysregulated phosphorylation of axonemal proteins, highlighting the critical role of kinase-mediated signaling in regulating sperm motility. Conversely, Dusp21 KO mice display no fertility or sperm motility defects, suggesting compensatory phosphatase activity. Phenotypic comparisons between Tekt1 and Tssk6 KO mice suggest their involvement in distinct subtypes of asthenozoospermia. Overall, this study elucidates how filamentous and enzymatic DMT proteins govern sperm function through divergent mechanisms, which have implications for molecular diagnosis of male infertility.
History
DepositionMay 16, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64625.png

Downloads & links

-
Map

FileDownload / File: emd_64625.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 764 pix.
= 710.52 Å		0.93 Å/pix.
x 764 pix.
= 710.52 Å		0.93 Å/pix.
x 764 pix.
= 710.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.008986995 - 0.012853909
Average (Standard dev.)0.000031748994 (±0.0009804661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions764764764
Spacing764764764
CellA=B=C: 710.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_64625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64625_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : sperm flagellar doublet microtubules

EntireName: sperm flagellar doublet microtubules
Components
  • Complex: sperm flagellar doublet microtubules

-
Supramolecule #1: sperm flagellar doublet microtubules

SupramoleculeName: sperm flagellar doublet microtubules / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

35823

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more