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- EMDB-1960: Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state -

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Entry
Database: EMDB / ID: 1960
TitleSymmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
KeywordsTRiC/CCT / chaperonin / cryo-EM / protein folding
SampleBovine TRiC/CCT in the nucleotide-free (apo) state
SourceBos taurus / mammal / bovine / ウシ /
Map datasymmetry-free apo-TRiC 3D reconstruction
Methodsingle particle reconstruction, at 10.5 Å resolution
AuthorsCong Y / Schroder GF / Meyer AS / Jakana J / Ma B / Dougherty MT / Schmid MF / Reissmann S / Levitt M / Ludtke SL / Frydman J / Chiu W
CitationEMBO J., 2012, 31, 720-730

EMBO J., 2012, 31, 720-730 Yorodumi Papers
Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu

Validation ReportPDB-ID: 4a0o

SummaryFull reportAbout validation report
DateDeposition: Sep 3, 2011 / Header (metadata) release: Feb 6, 2012 / Map release: Feb 6, 2012 / Last update: Mar 20, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.13
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 1.13
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4a0o
  • Surface level: 1.13
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_1960.map.gz (map file in CCP4 format, 11665 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.4 Å/pix.
= 345.6 Å
144 pix
2.4 Å/pix.
= 345.6 Å
144 pix
2.4 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.4 Å
Density
Contour Level:1.13 (by author), 1.13 (movie #1):
Minimum - Maximum-0.42493957 - 2.51474524
Average (Standard dev.)0.07473919 (0.28258339)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 345.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.4252.5150.075

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Supplemental data

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Sample components

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Entire Bovine TRiC/CCT in the nucleotide-free (apo) state

EntireName: Bovine TRiC/CCT in the nucleotide-free (apo) state / Number of components: 1 / Oligomeric State: 16-mer
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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Component #1: protein, bovine TRiC

ProteinName: bovine TRiC / a.k.a: TRiC or CCT / Oligomeric Details: 16-mer / Recombinant expression: No
MassTheoretical: 1000 kDa / Experimental: 1000 kDa
SourceSpecies: Bos taurus / mammal / bovine / ウシ /
Source (natural)Organ or tissue: Testes

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Support film200-mesh Quantifoil holey grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 100 % / Method: Two-side blotting for 1 second before plunging / Details: Vitrification instrument: FEI vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Oct 20, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Astigmatism: objective lens astigmatism correction / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3000 nm / Energy filter: JEOL in-column omega energy filter / Energy window: 0-20 eV
Specimen HolderHolder: Side entry / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 101 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 700 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 47151 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: EMAN1.8 / CTF correction: each micrograph
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
Resolution: 10.5 Å / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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