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- EMDB-1961: Symmetry-free cryo-EM map of TRiC-AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: 1961
TitleSymmetry-free cryo-EM map of TRiC-AMP-PNP
KeywordsTRiC/CCT / chaperonin / cryo-EM / protein folding
Samplebovine TRiC/CCT in the AMP-PNP state
SourceBos taurus / mammal / bovine / ウシ /
Map datasymmetry-free cryo-EM density of TRiC-AMP-PNP
Methodsingle particle reconstruction, at 10.7 A 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 StrPapers
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

DateDeposition: Sep 5, 2011 / Header (metadata) release: Feb 6, 2012 / Map release: Feb 6, 2012 / Last update: Sep 5, 2011

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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-4a0v
  • Surface level: 1.13
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1961.map.gz (map file in CCP4 format, 11665 KB)
Projections & slices
Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.4 A/pix
= 345.6 A
144 pix
2.4 A/pix
= 345.6 A
144 pix
2.4 A/pix
= 345.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.4 A
Density
Contour Level:1.13 (by author), 1.13 (movie #1):
Minimum - Maximum-0.37267885 - 2.16418886
Average (Standard dev.)0.06878981 (0.26539356)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 345.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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-0.3732.1640.069

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Supplemental data

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Sample components

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Entire bovine TRiC/CCT in the AMP-PNP state

EntireName: bovine TRiC/CCT in the AMP-PNP state / Number of components: 2 / 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 /

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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
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/A2 / 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: 29374 / 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: 10.7 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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