+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26089 | ||||||||||||
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Title | The beta-tubulin folding intermediate I | ||||||||||||
Map data | Sharpened map. The beta-tubulin folding intermediate with folded N domain in closed TRiC chamber. | ||||||||||||
Sample |
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Keywords | Human chaperonin TRiC with beta-tubulin folding intermediate I / CHAPERONE | ||||||||||||
Function / homology | Function and homology information odontoblast differentiation / scaRNA localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / chaperone mediated protein folding independent of cofactor / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / binding of sperm to zona pellucida ...odontoblast differentiation / scaRNA localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / chaperone mediated protein folding independent of cofactor / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / chaperonin-containing T-complex / Prefoldin mediated transfer of substrate to CCT/TriC / GTPase activating protein binding / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / natural killer cell mediated cytotoxicity / WD40-repeat domain binding / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / pericentriolar material / MHC class I protein binding / beta-tubulin 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein folding chaperone / positive regulation of telomere maintenance via telomerase / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / 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 / mitotic spindle / cilium / structural constituent of cytoskeleton / mRNA 5'-UTR binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / azurophil granule lumen / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / G-protein beta-subunit binding / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / 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 / GTP binding / protein-containing complex 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Zhao Y / Frydman J / Chiu W | ||||||||||||
Funding support | United States, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26089.map.gz | 112 MB | EMDB map data format | |
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Header (meta data) | emd-26089-v30.xml emd-26089.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
Images | emd_26089.png | 108 KB | ||
Filedesc metadata | emd-26089.cif.gz | 9.5 KB | ||
Others | emd_26089_additional_1.map.gz | 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26089 | HTTPS FTP |
-Validation report
Summary document | emd_26089_validation.pdf.gz | 637.3 KB | Display | EMDB validaton report |
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Full document | emd_26089_full_validation.pdf.gz | 636.9 KB | Display | |
Data in XML | emd_26089_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_26089_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26089 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26089 | HTTPS FTP |
-Related structure data
Related structure data | 7trgMC 7ttnC 7tttC 7tubC 7wu7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26089.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map. The beta-tubulin folding intermediate with folded N domain in closed TRiC chamber. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_26089_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Closed form human TRiC in complex with beta-tubulin under ATP/AlF...
+Supramolecule #1: Closed form human TRiC in complex with beta-tubulin under ATP/AlF...
+Macromolecule #1: Tubulin beta chain
+Macromolecule #2: T-complex protein 1 subunit theta
+Macromolecule #3: T-complex protein 1 subunit eta
+Macromolecule #4: T-complex protein 1 subunit epsilon
+Macromolecule #5: T-complex protein 1 subunit beta
+Macromolecule #6: T-complex protein 1 subunit delta
+Macromolecule #7: T-complex protein 1 subunit alpha
+Macromolecule #8: T-complex protein 1 subunit gamma
+Macromolecule #9: T-complex protein 1 subunit zeta
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #12: ALUMINUM FLUORIDE
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.21 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110984 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7trg: |