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Yorodumi- EMDB-5148: 4.0 Angstrom two-fold imposed cryo-EM map of TRiC in the both-rin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5148 | |||||||||
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Title | 4.0 Angstrom two-fold imposed cryo-EM map of TRiC in the both-ring closed ATP-AlFx state | |||||||||
Map data | 4.0 Angstrom two-fold imposed cryo-EM map of bovine TRiC in the closed conformation | |||||||||
Sample |
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Keywords | TRiC/CCT / Asymmetric / Cryo-EM / structure | |||||||||
Function / homology | Function and homology information Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / chaperone-mediated protein folding ...Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / cilium / unfolded protein binding / melanosome / protein folding / cell body / microtubule / protein stabilization / centrosome / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Cong Y / Baker ML / Jakana J / Woolford D / Miller EJ / Reissmann S / Kumar RN / Redding-Johanson AM / Batth TS / Mukhopadhyay A ...Cong Y / Baker ML / Jakana J / Woolford D / Miller EJ / Reissmann S / Kumar RN / Redding-Johanson AM / Batth TS / Mukhopadhyay A / Ludtke SJ / Frydman J / Chiu W | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Authors: Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / ...Authors: Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / Steven J Ludtke / Judith Frydman / Wah Chiu / Abstract: The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates ...The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity. | |||||||||
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_5148.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-5148-v30.xml emd-5148.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_5148_1.png | 1.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5148 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5148 | HTTPS FTP |
-Validation report
Summary document | emd_5148_validation.pdf.gz | 300.3 KB | Display | EMDB validaton report |
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Full document | emd_5148_full_validation.pdf.gz | 299.9 KB | Display | |
Data in XML | emd_5148_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5148 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5148 | HTTPS FTP |
-Related structure data
Related structure data | 3iygMC 3kttMC 5145C M: atomic model generated by this map C: citing same article (ref.) |
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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_5148.map.gz / Format: CCP4 / Size: 31.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 4.0 Angstrom two-fold imposed cryo-EM map of bovine TRiC in the closed conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : bovine TRiC (also called CCT)
Entire | Name: bovine TRiC (also called CCT) |
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Components |
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-Supramolecule #1000: bovine TRiC (also called CCT)
Supramolecule | Name: bovine TRiC (also called CCT) / type: sample / ID: 1000 / Number unique components: 8 |
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Molecular weight | Experimental: 500 KDa / Theoretical: 450 KDa |
-Macromolecule #1: TRiC or CCT
Macromolecule | Name: TRiC or CCT / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC or CCT / Number of copies: 8 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: bovine |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: 200-mesh Quantifoil holey grid |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 101 K / Instrument: OTHER / Method: two-side blotting for 1 second before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 101 K / Average: 101 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism correction |
Specialist optics | Energy filter - Name: in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Aug 1, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1500 / Average electron dose: 18 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps Number images used: 101000 |