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- PDB-9unw: mouse PDCD5-TRiC complex -

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Basic information

Entry
Database: PDB / ID: 9unw
Titlemouse PDCD5-TRiC complex
Components
  • (T-complex protein 1 subunit ...) x 8
  • Programmed cell death protein 5
KeywordsCHAPERONE / Complex / cofactor
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / RHOBTB1 GTPase cycle / negative regulation of protein folding / RHOBTB2 GTPase cycle / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex ...Association of TriC/CCT with target proteins during biosynthesis / RHOBTB1 GTPase cycle / negative regulation of protein folding / RHOBTB2 GTPase cycle / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / binding of sperm to zona pellucida / acetyltransferase activator activity / WD40-repeat domain binding / pericentriolar material / microtubule organizing center / cellular response to transforming growth factor beta stimulus / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / beta-tubulin binding / heterochromatin / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / protein folding chaperone / acrosomal vesicle / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / response to virus / melanosome / unfolded protein binding / myelin sheath / G-protein beta-subunit binding / heparin binding / protein folding / cell body / regulation of apoptotic process / microtubule / protein stabilization / positive regulation of apoptotic process / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / centrosome / Golgi apparatus / ATP hydrolysis activity / mitochondrion / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit ...PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
T-complex protein 1 subunit alpha / T-complex protein 1 subunit theta / Programmed cell death protein 5 / T-complex protein 1 subunit eta / T-complex protein 1 subunit beta / T-complex protein 1 subunit delta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit zeta / T-complex protein 1 subunit gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsSong, Q.Q. / Cong, Y.
Funding support China, 1items
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
DepositionApr 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: T-complex protein 1 subunit alpha
G: T-complex protein 1 subunit beta
H: T-complex protein 1 subunit gamma
I: T-complex protein 1 subunit delta
F: T-complex protein 1 subunit epsilon
A: T-complex protein 1 subunit zeta
B: T-complex protein 1 subunit eta
E: T-complex protein 1 subunit theta
D: Programmed cell death protein 5


Theoretical massNumber of molelcules
Total (without water)493,1219
Polymers493,1219
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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T-complex protein 1 subunit ... , 8 types, 8 molecules CGHIFABE

#1: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha / Tailless complex polypeptide 1A / TCP-1-A / Tailless complex polypeptide ...TCP-1-alpha / CCT-alpha / Tailless complex polypeptide 1A / TCP-1-A / Tailless complex polypeptide 1B / TCP-1-B


Mass: 60524.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P11983, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57556.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80314, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / Matricin / mTRiC-P5


Mass: 60710.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80318, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#4: Protein T-complex protein 1 subunit delta / TCP-1-delta / A45 / CCT-delta


Mass: 58138.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80315, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#5: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 59704.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80316, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#6: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta-1


Mass: 58086.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80317, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#7: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta


Mass: 59727.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P80313, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#8: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta


Mass: 59625.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P42932, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Protein , 1 types, 1 molecules D

#9: Protein Programmed cell death protein 5 / TF-1 cell apoptosis-related protein 19 / Protein TFAR19


Mass: 19048.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd5, Tfar19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56812

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse PDCD5-TRiC complex / Type: COMPLEX / Entity ID: #9 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 15000 nm / Nominal defocus min: 9000 nm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659930 / Symmetry type: POINT

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