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Yorodumi- EMDB-12607: Human TRiC complex in closed state with nanobody and tubulin bound -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12607 | |||||||||
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Title | Human TRiC complex in closed state with nanobody and tubulin bound | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere ...Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / chaperonin-containing T-complex / Gap junction assembly / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Assembly and cell surface presentation of NMDA receptors / RHOBTB1 GTPase cycle / COPI-dependent Golgi-to-ER retrograde traffic / intermediate filament cytoskeleton / WD40-repeat domain binding / beta-tubulin binding / pericentriolar material / Recycling pathway of L1 / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / RHO GTPases activate IQGAPs / Hedgehog 'off' state / heterochromatin / RHOBTB2 GTPase cycle / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / chaperone-mediated protein folding / Mitotic Prometaphase / protein folding chaperone / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ATP-dependent protein folding chaperone / neuron migration / response to virus / mRNA 5'-UTR binding / cilium / structural constituent of cytoskeleton / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Separation of Sister Chromatids / G-protein beta-subunit binding / extracellular vesicle / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / melanosome / unfolded protein binding / protein folding / mitotic cell cycle / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / protein stabilization / cytoskeleton / cadherin binding / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Kelly JJ / Chi G / Bulawa C / Paavilainen VO / Bountra C / Huiskonen JT / Yue W | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Snapshots of actin and tubulin folding inside the TRiC chaperonin. Authors: John J Kelly / Dale Tranter / Els Pardon / Gamma Chi / Holger Kramer / Lotta Happonen / Kelly M Knee / Jay M Janz / Jan Steyaert / Christine Bulawa / Ville O Paavilainen / Juha T Huiskonen / Wyatt W Yue / Abstract: The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, ...The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12607.map.gz | 228.5 MB | EMDB map data format | |
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Header (meta data) | emd-12607-v30.xml emd-12607.xml | 29.8 KB 29.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12607_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_12607.png | 215.6 KB | ||
Masks | emd_12607_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12607_half_map_1.map.gz emd_12607_half_map_2.map.gz | 194 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12607 | HTTPS FTP |
-Related structure data
Related structure data | 7nvnMC 7nvlC 7nvmC 7nvoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12607.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12607_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12607_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12607_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human type II chaperonin TRiC/CCT complex with nanobody Nb18 and ...
+Supramolecule #1: Human type II chaperonin TRiC/CCT complex with nanobody Nb18 and ...
+Supramolecule #2: Human type II chaperonin TRiC/CCT complex
+Supramolecule #3: Nanobody
+Supramolecule #4: T-complex protein 1 subunit epsilon
+Macromolecule #1: T-complex protein 1 subunit alpha
+Macromolecule #2: T-complex protein 1 subunit beta
+Macromolecule #3: T-complex protein 1 subunit delta
+Macromolecule #4: T-complex protein 1 subunit epsilon
+Macromolecule #5: T-complex protein 1 subunit gamma
+Macromolecule #6: T-complex protein 1 subunit eta
+Macromolecule #7: Nanobody
+Macromolecule #8: T-complex protein 1 subunit theta
+Macromolecule #9: T-complex protein 1 subunit zeta
+Macromolecule #10: Tubulin beta-2A chain
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ALUMINUM FLUORIDE
+Macromolecule #14: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |