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- PDB-8i9q: The focused refinement of CCT4-PhLP2A from TRiC-PhLP2A complex in... -

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Basic information

Entry
Database: PDB / ID: 8i9q
TitleThe focused refinement of CCT4-PhLP2A from TRiC-PhLP2A complex in the open state
Components
  • Phosducin-like protein 3
  • T-complex protein 1 subunit delta
KeywordsCHAPERONE / chaperonin complex / cochaperone
Function / homology
Function and homology information


negative regulation of chaperone-mediated protein folding / perinucleolar compartment / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC ...negative regulation of chaperone-mediated protein folding / perinucleolar compartment / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / vascular endothelial growth factor receptor 2 binding / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein folding / regulation of peptidyl-tyrosine phosphorylation / protein folding chaperone / : / positive regulation of endothelial cell proliferation / positive regulation of telomere maintenance via telomerase / negative regulation of ubiquitin-dependent protein catabolic process / cell projection / ATP-dependent protein folding chaperone / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of angiogenesis / unfolded protein binding / melanosome / protein folding / cell body / actin cytoskeleton organization / angiogenesis / microtubule / protein stabilization / centrosome / apoptotic process / positive regulation of gene expression / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Phosducin, thioredoxin-like domain / Phosducin / T-complex protein 1, delta 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 ...Phosducin, thioredoxin-like domain / Phosducin / T-complex protein 1, delta 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
T-complex protein 1 subunit delta / Phosducin-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsRoh, S.H. / Park, J. / Kim, H. / Lim, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle.
Authors: Junsun Park / Hyunmin Kim / Daniel Gestaut / Seyeon Lim / Kwadwo A Opoku-Nsiah / Alexander Leitner / Judith Frydman / Soung-Hun Roh /
Abstract: Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin- ...Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: T-complex protein 1 subunit delta
Q: Phosducin-like protein 3


Theoretical massNumber of molelcules
Total (without water)85,6462
Polymers85,6462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


Mass: 57996.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT4, CCTD, SRB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50991
#2: Protein Phosducin-like protein 3 / PhPL3


Mass: 27650.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCL3, PhLP2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2J4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of human TRiC/CCT-PhLP2ACOMPLEXall0RECOMBINANT
2T-complex protein 1 subunit delta from human TRiC/CCT complexCOMPLEX#11RECOMBINANT
3PhLP2A (PDCL3)COMPLEX#21RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
12Trichoplusia ni (cabbage looper)7111high fivepFastbac-dual
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium chlorideNaCl1
21 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 15075
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2.0particle selectioncryoSPARC was used for 2D classification
4cryoSPARC3.2.0CTF correctioncryoSPARC was used for the CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.19model refinementPhenix was used for refinement
10Coot0.9.6model refinement
11cryoSPARC3.2.0initial Euler assignment
12cryoSPARC3.2.0final Euler assignment
13cryoSPARC3.2.0classification
14cryoSPARC3.2.03D reconstruction
CTF correctionDetails: CTF correction was performed for every micrographs / Type: NONE
Particle selectionNum. of particles selected: 2691733
Details: The initial particle selection after 2D class classification
3D reconstructionResolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 485964 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6NR8

6nr8


Accession code: 6NR8 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055234
ELECTRON MICROSCOPYf_angle_d0.8037061
ELECTRON MICROSCOPYf_dihedral_angle_d4.9923274
ELECTRON MICROSCOPYf_chiral_restr0.049861
ELECTRON MICROSCOPYf_plane_restr0.006893

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