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Yorodumi- EMDB-12606: Human TRiC complex in closed state with nanobody Nb18, actin and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12606 | |||||||||
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Title | Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information basal body patch / negative regulation of chaperone-mediated protein folding / perinucleolar compartment / tight junction assembly / regulation of transepithelial transport / zona pellucida receptor complex / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / scaRNA localization to Cajal body / morphogenesis of a polarized epithelium ...basal body patch / negative regulation of chaperone-mediated protein folding / perinucleolar compartment / tight junction assembly / regulation of transepithelial transport / zona pellucida receptor complex / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / scaRNA localization to Cajal body / morphogenesis of a polarized epithelium / profilin binding / positive regulation of protein localization to Cajal body / tubulin complex assembly / Formation of annular gap junctions / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / Gap junction degradation / BBSome-mediated cargo-targeting to cilium / dense body / Cell-extracellular matrix interactions / chaperonin-containing T-complex / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / vascular endothelial growth factor receptor 2 binding / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of stress fiber assembly / Adherens junctions interactions / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / sarcomere organization / NuA4 histone acetyltransferase complex / WD40-repeat domain binding / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / maintenance of blood-brain barrier / positive regulation of wound healing / myofibril / beta-tubulin binding / pericentriolar material / Recycling pathway of L1 / filamentous actin / Association of TriC/CCT with target proteins during biosynthesis / calyx of Held / EPH-ephrin mediated repulsion of cells / chaperone-mediated protein complex assembly / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / heterochromatin / RHOBTB2 GTPase cycle / phagocytic vesicle / chaperone-mediated protein folding / protein folding chaperone / regulation of peptidyl-tyrosine phosphorylation / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of endothelial cell proliferation / axonogenesis / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / actin filament / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to virus / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / mRNA 5'-UTR binding / cilium / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / azurophil granule lumen / melanosome / cell-cell junction / unfolded protein binding / Signaling by BRAF and RAF1 fusions / protein folding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kelly JJ / Chi G / Bulawa C / Paavilainen VO / Bountra C / Huiskonen JT / Yue W / Structural Genomics Consortium (SGC) | |||||||||
Funding support | United Kingdom, Finland, 2 items
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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_12606.map.gz | 229 MB | EMDB map data format | |
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Header (meta data) | emd-12606-v30.xml emd-12606.xml | 31.3 KB 31.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12606_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_12606.png | 213 KB | ||
Masks | emd_12606_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12606_half_map_1.map.gz emd_12606_half_map_2.map.gz | 194.1 MB 194.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12606 | HTTPS FTP |
-Related structure data
Related structure data | 7nvmMC 7nvlC 7nvnC 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_12606.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_12606_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12606_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12606_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, act...
+Supramolecule #1: Human type II chaperonin TRiC/CCT complex with nanobody Nb18, act...
+Supramolecule #2: Human type II chaperonin TRiC/CCT
+Supramolecule #3: T-complex protein
+Supramolecule #4: Nanobody
+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 Nb18
+Macromolecule #8: T-complex protein 1 subunit theta
+Macromolecule #9: T-complex protein 1 subunit zeta
+Macromolecule #10: Actin, cytoplasmic 2
+Macromolecule #11: Phosducin-like protein 3
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #13: MAGNESIUM ION
+Macromolecule #14: ALUMINUM FLUORIDE
+Macromolecule #15: 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 |