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- EMDB-5145: 4.7 Angstrom asymmetric cryo-EM map of TRiC in the both-ring clos... -

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Basic information

Entry
Database: EMDB / ID: EMD-5145
Title4.7 Angstrom asymmetric cryo-EM map of TRiC in the both-ring closed ATP-AlFx state
Map data4.7 Angstrom asymmetric cryo-EM map of TRiC in the bot-ring closed ATP-AlFx state
Sample
  • Sample: bovine TRiC (also called CCT)
  • Protein or peptide: bovine TRiC
KeywordsTRiC / 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 / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / ATP-dependent protein folding chaperone / cilium / unfolded protein binding / melanosome ...Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / ATP-dependent protein folding chaperone / cilium / unfolded protein binding / melanosome / protein folding / centrosome / ATP hydrolysis activity / ATP binding
Similarity search - Function
T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. ...T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
T-complex protein 1 subunit eta / T-complex protein 1 subunit delta / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit beta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsCong 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
CitationJournal: 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
DepositionNov 28, 2009-
Header (metadata) releaseMar 8, 2010-
Map releaseMar 8, 2010-
UpdateSep 27, 2011-
Current statusSep 27, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.53
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.53
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyg
  • Surface level: 2.53
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3ktt
  • Surface level: 2.53
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyg
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3ktt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5145_1.png

Downloads & links

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Map

FileDownload / File: emd_5145.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4.7 Angstrom asymmetric cryo-EM map of TRiC in the bot-ring closed ATP-AlFx state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.53 / Movie #1: 2.53
Minimum - Maximum-5.02971 - 5.97423
Average (Standard dev.)0.0724917 (±0.477697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-5.0305.9740.072

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Supplemental data

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Sample components

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Entire : bovine TRiC (also called CCT)

EntireName: bovine TRiC (also called CCT)
Components
  • Sample: bovine TRiC (also called CCT)
  • Protein or peptide: bovine TRiC

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Supramolecule #1000: bovine TRiC (also called CCT)

SupramoleculeName: bovine TRiC (also called CCT) / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 8
Molecular weightExperimental: 1.0 MDa / Theoretical: 1.0 MDa

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Macromolecule #1: bovine TRiC

MacromoleculeName: bovine TRiC / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC or CCT / Oligomeric state: 16-mer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

GridDetails: 200-mesh Quantifoil holey grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 101 K / Instrument: OTHER / Method: two-side blotting for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 101 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism correction
Specialist opticsEnergy filter - Name: in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateAug 1, 2008
Image recordingCategory: 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder: side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsA recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.7 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

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