[English] 日本語
Yorodumi
- EMDB-62236: TRiC from bovine flagella, focused refinement on one-ring -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62236
TitleTRiC from bovine flagella, focused refinement on one-ring
Map dataBovine-flagellar-TRiC_one_ring_focused-sharpen map
Sample
  • Complex: TRiC purified from bovine sperm flagella
KeywordsTRiC / sperm / flagella / motile cilia / CHAPERONE
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsMeng X / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Mol Cell / Year: 2026
Title: Chaperonin TRiC bridges radial spokes for folding locally translated proteins to sustain mammalian sperm flagellar motility.
Authors: Xueming Meng / Luan Li / Cheng Lin / Yun Zhu / Yanyan Feng / Qun Zhao / Nan Zhao / Xuehai Zhou / Yujie Tong / Shanshan Wang / Guoliang Yin / Ruimin Liu / Lihua Zhang / Fei Sun / Xiumin Yan / ...Authors: Xueming Meng / Luan Li / Cheng Lin / Yun Zhu / Yanyan Feng / Qun Zhao / Nan Zhao / Xuehai Zhou / Yujie Tong / Shanshan Wang / Guoliang Yin / Ruimin Liu / Lihua Zhang / Fei Sun / Xiumin Yan / Xueliang Zhu / Yao Cong /
Abstract: As animals evolved from external to internal fertilization, sperm flagella, once transiently propelling sperm in water to reach nearby eggs, developed to beat for days in the viscous female ...As animals evolved from external to internal fertilization, sperm flagella, once transiently propelling sperm in water to reach nearby eggs, developed to beat for days in the viscous female reproductive tract. How flagella are remodeled accordingly remains unclear. Unlike externally fertilizing zebrafish and sea urchins, mammalian flagella feature a barrel between radial spokes (RSs) RS1 and RS2. Here, we show that this RS1-RS2 barrel (RRB) is a unique T-complex protein-1 ring complex (TRiC) that folds locally translated polypeptides to sustain flagellar motility. Cryo-electron microscopy (cryo-EM) reveals a flagellum-specific TRiC structure. An in situ cryo-electron tomography (cryo-ET) map of flagellar axonemes captures the RRB TRiC in an active, substrate-receptive state, with additional densities suggestive of folding substrates and cofactors. Mammalian flagella contain components of translation machineries and locally synthesize proteins. Cross-linking mass spectrometry identifies candidate locally translated axonemal proteins and folding substrates. Furthermore, a TRiC ATPase inhibitor markedly represses mouse sperm motility. Our findings provide insights into flagellar remodeling in internally fertilizing species.
History
DepositionOct 31, 2024-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62236.png

Downloads & links

-
Map

FileDownload / File: emd_62236.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBovine-flagellar-TRiC_one_ring_focused-sharpen map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 346.28 Å		0.87 Å/pix.
x 400 pix.
= 346.28 Å		0.87 Å/pix.
x 400 pix.
= 346.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-0.09990665 - 12.495748499999999
Average (Standard dev.)0.049903315 (±0.46461782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 346.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62236_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Bovine-flagellar-TRiC one-ring focused-refine map

Fileemd_62236_additional_1.map
AnnotationBovine-flagellar-TRiC_one-ring_focused-refine_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Bovine-flagellar-TRiC one-ring focused-refine map J840 map half B

Fileemd_62236_half_map_1.map
AnnotationBovine-flagellar-TRiC_one-ring_focused-refine_map_J840_map_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Bovine-flagellar-TRiC one-ring focused-refine map J840 map half A

Fileemd_62236_half_map_2.map
AnnotationBovine-flagellar-TRiC_one-ring_focused-refine_map_J840_map_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TRiC purified from bovine sperm flagella

EntireName: TRiC purified from bovine sperm flagella
Components
  • Complex: TRiC purified from bovine sperm flagella

-
Supramolecule #1: TRiC purified from bovine sperm flagella

SupramoleculeName: TRiC purified from bovine sperm flagella / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86676
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