+Open data
-Basic information
Entry | Database: PDB / ID: 7wu7 | ||||||
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Title | Prefoldin-tubulin-TRiC complex | ||||||
Components |
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Keywords | CHAPERONE / chapronin complex | ||||||
Function / homology | Function and homology information RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly / RPAP3/R2TP/prefoldin-like complex / 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 / RNA polymerase II core complex assembly / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / negative regulation of amyloid fibril formation / protein folding chaperone complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / microtubule-based process / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / : / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / tubulin binding / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / negative regulation of canonical Wnt signaling pathway / mRNA 5'-UTR binding / cilium / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transcription corepressor activity / G-protein beta-subunit binding / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / retina development in camera-type eye / amyloid-beta binding / protein-folding chaperone binding / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cadherin binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å | ||||||
Authors | Gestaut, D. / Zhao, Y. / Park, J. / Ma, B. / Leitner, A. / Collier, M. / Pintilie, G. / Roh, S.-H. / Chiu, W. / Frydman, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Cell / Year: 2022 Title: Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Authors: Daniel Gestaut / Yanyan Zhao / Junsun Park / Boxue Ma / Alexander Leitner / Miranda Collier / Grigore Pintilie / Soung-Hun Roh / Wah Chiu / Judith Frydman / Abstract: The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of ...The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wu7.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7wu7.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7wu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wu7_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7wu7_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7wu7_validation.xml.gz | 246.1 KB | Display | |
Data in CIF | 7wu7_validation.cif.gz | 364.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wu7 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wu7 | HTTPS FTP |
-Related structure data
Related structure data | 32823MC 7trgC 7ttnC 7tttC 7tubC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Prefoldin subunit ... , 6 types, 6 molecules 123456
#1: Protein | Mass: 14234.497 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN1, PFD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60925 |
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#2: Protein | Mass: 16672.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN2, PFD2, HSPC231 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UHV9 |
#3: Protein | Mass: 22658.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VBP1, PFDN3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61758 |
#4: Protein | Mass: 16160.071 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN4, PFD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NQP4 |
#5: Protein | Mass: 16051.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN5, MM1, PFD5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99471 |
#6: Protein | Mass: 14603.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN6, HKE2, PFD6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O15212 |
-T-complex protein 1 subunit ... , 8 types, 16 molecules AIBJCKDLEMFNGOHP
#7: Protein | Mass: 60418.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCP1, CCT1, CCTA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17987 #8: Protein | Mass: 57567.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT2, 99D8.1, CCTB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78371 #9: Protein | Mass: 60613.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49368 #10: Protein | Mass: 57996.113 Da / Num. of mol.: 2 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 #11: Protein | Mass: 59749.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48643 #12: Protein | Mass: 58166.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40227 #13: Protein | Mass: 59443.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT7, CCTH, NIP7-1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99832 #14: Protein | Mass: 59576.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ, KIAA0002 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50990 |
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-Non-polymers , 1 types, 4 molecules
#15: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: high five / Plasmid: pFastbac-dual | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 11796 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: CTF correction was performed for every micrographs / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 443858 Details: The initial particle selection after 2D class classification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194013 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6NR8 Accession code: 6NR8 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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