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- EMDB-66412: mouse PDCD5-TRiC-ADP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66412
Titlemouse PDCD5-TRiC-ADP complex
Map data
Sample
  • Complex: mouse PDCD5-TRiC-ADP complex
KeywordsComplex / cofactor / CHAPERONE
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsSong QQ / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Cell / Year: 2026
Title: PDCD5 promotes substrate release from the TRiC complex in cilia and flagella.
Authors: Huafang Wei / Qianqian Song / Liying Wang / Qiong Deng / Bingbing Wu / Yinghong Chen / Tingting Han / Yueshuai Guo / Zuyang Li / Fucheng Dong / Shuang Ma / Qiaoyu Zhao / Xiangyi Shi / Chen ...Authors: Huafang Wei / Qianqian Song / Liying Wang / Qiong Deng / Bingbing Wu / Yinghong Chen / Tingting Han / Yueshuai Guo / Zuyang Li / Fucheng Dong / Shuang Ma / Qiaoyu Zhao / Xiangyi Shi / Chen Pan / Wanying Jiang / Xiaofei Liu / Yingyu Chen / Renjie Jiao / Li Yuan / Chao Liu / Xuejiang Guo / Yao Cong / Wei Li /
Abstract: Approximately 10% of eukaryotic proteins are folded by the TRiC/CCT complex (TCP1-ring complex, also called CCT for cytosolic chaperonin containing TCP1), and only open-state TRiC can bind with ...Approximately 10% of eukaryotic proteins are folded by the TRiC/CCT complex (TCP1-ring complex, also called CCT for cytosolic chaperonin containing TCP1), and only open-state TRiC can bind with programmed cell death 5 (PDCD5). However, the physiological role of the PDCD5-TRiC interaction remains elusive. Here, we show that PDCD5 is required for flagellum biogenesis and ciliogenesis and present the PDCD5-TRiC structures in their open states at near-atomic resolution. Mechanically, we find that PDCD5 promotes substrates release by competing with PhLP2A to interact with TRiC, and the depletion of PDCD5 traps flagellum- and cilium-associated proteins within TRiC, finally leading to malformed flagella of spermatids and cilia in mouse ciliated cells. Moreover, we demonstrate that the function of PDCD5 in flagellum biogenesis and ciliogenesis depends on the interaction with TRiC by its C terminus. These findings identify PDCD5 as a TRiC regulator to promote a subset of proteins release.
History
DepositionSep 29, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66412.png

Downloads & links

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Map

FileDownload / File: emd_66412.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
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Contour LevelBy AUTHOR: 2.99
Minimum - Maximum-0.10759765 - 14.854759
Average (Standard dev.)0.0398829 (±0.6443429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66412_msk_1.map
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Additional map: #1

Fileemd_66412_additional_1.map
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Half map: #1

Fileemd_66412_half_map_1.map
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Half map: #2

Fileemd_66412_half_map_2.map
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Sample components

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Entire : mouse PDCD5-TRiC-ADP complex

EntireName: mouse PDCD5-TRiC-ADP complex
Components
  • Complex: mouse PDCD5-TRiC-ADP complex

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Supramolecule #1: mouse PDCD5-TRiC-ADP complex

SupramoleculeName: mouse PDCD5-TRiC-ADP complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

32993

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 194789
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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