+Open data
-Basic information
Entry | Database: PDB / ID: 7ttt | ||||||||||||
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Title | The beta-tubulin folding intermediate III | ||||||||||||
Components |
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Keywords | CHAPERONE / Human chaperonin TRiC with beta-tubulin folding intermediate III | ||||||||||||
Function / homology | Function and homology information odontoblast differentiation / 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 / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / Folding of actin by CCT/TriC ...odontoblast differentiation / 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 / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / 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 / natural killer cell mediated cytotoxicity / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / GTPase activating protein binding / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / pericentriolar material / beta-tubulin binding / MHC class I protein binding / Association of TriC/CCT with target proteins during biosynthesis / microtubule-based process / chaperone-mediated protein complex assembly / spindle assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / AURKA Activation by TPX2 / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / structural constituent of cytoskeleton / mitotic spindle / mRNA 5'-UTR binding / cilium / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / Potential therapeutics for SARS / cytoskeleton / protein stabilization / cadherin binding / membrane raft / protein domain specific binding / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Zhao, Y. / Frydman, J. / Chiu, W. | ||||||||||||
Funding support | United States, 3items
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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 | 7ttt.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ttt.ent.gz | 708.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ttt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ttt_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ttt_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ttt_validation.xml.gz | 111 KB | Display | |
Data in CIF | 7ttt_validation.cif.gz | 169.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7ttt ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7ttt | HTTPS FTP |
-Related structure data
Related structure data | 26123MC 7trgC 7ttnC 7tubC 7wu7C C: citing same article (ref.) M: map data used to model this data |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49717.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB, TUBB5, OK/SW-cl.56 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07437 |
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-T-complex protein 1 subunit ... , 8 types, 8 molecules BCDEFGHI
#2: Protein | Mass: 59576.332 Da / Num. of mol.: 1 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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#3: Protein | Mass: 60560.672 Da / Num. of mol.: 1 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 |
#4: Protein | Mass: 59749.957 Da / Num. of mol.: 1 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 |
#5: Protein | Mass: 57567.141 Da / Num. of mol.: 1 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 |
#6: Protein | 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 |
#7: Protein | Mass: 60418.477 Da / Num. of mol.: 1 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: 60613.855 Da / Num. of mol.: 1 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 |
#9: Protein | Mass: 58166.180 Da / Num. of mol.: 1 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 |
-Non-polymers , 4 types, 32 molecules
#10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-ADP / #12: Chemical | ChemComp-AF3 / #13: Water | ChemComp-HOH / | |
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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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Closed form human TRiC in complex with beta-tubulin under ATP/AlFx condition. Type: COMPLEX / Entity ID: #9, #2-#4, #6-#8, #5, #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Strain: High Five / Cell: ovarian cells | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1.21 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94955 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |