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- EMDB-9540: Structure of Yeast NPP-TRiC -

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Basic information

Entry
Database: EMDB / ID: 9540
TitleStructure of Yeast NPP-TRiC
SampleYeast NPP-TRiC
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map dataYeast NPP-TRiC at 4.7 angstroms resolution
Methodsingle particle reconstruction, at 4.7 Å resolution
AuthorsZang Y / Jin M / Wang H / Cong Y
CitationNat. Struct. Mol. Biol., 2016, 23, 1083-1091

Nat. Struct. Mol. Biol., 2016, 23, 1083-1091 Yorodumi Papers
Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM.
Yunxiang Zang / Mingliang Jin / Huping Wang / Zhicheng Cui / Liangliang Kong / Caixuan Liu / Yao Cong

Validation ReportPDB-ID: 5gw4

SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Oct 26, 2016 / Last update: Oct 26, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.887
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.887
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5gw4
  • Surface level: 0.887
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_9540.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.408 Å
256 pix
1.32 Å/pix.
= 337.408 Å
256 pix
1.32 Å/pix.
= 337.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.318 Å
Density
Contour Level:0.887 (by author), 0.887 (movie #1):
Minimum - Maximum-1.5254954 - 3.027191
Average (Standard dev.)0.027203212 (0.15941684)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 337.408 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.408337.408337.408
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-1.5253.0270.027

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Supplemental data

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Sample components

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Entire Yeast NPP-TRiC

EntireName: Yeast NPP-TRiC / Details: nucleotide partially preloaded yTRiC / Number of components: 17
MassTheoretical: 960 kDa

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Component #1: protein, Yeast NPP-TRiC

ProteinName: Yeast NPP-TRiC / Details: nucleotide partially preloaded yTRiC / Recombinant expression: No
MassTheoretical: 960 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: S288c

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Component #2: protein, T-complex protein 1 subunit alpha

ProteinName: T-complex protein 1 subunit alpha / Recombinant expression: No

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Component #3: protein, T-complex protein 1 subunit beta

ProteinName: T-complex protein 1 subunit beta / Recombinant expression: No

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Component #4: protein, T-complex protein 1 subunit delta

ProteinName: T-complex protein 1 subunit delta / Recombinant expression: No

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Component #5: protein, T-complex protein 1 subunit epsilon

ProteinName: T-complex protein 1 subunit epsilon / Recombinant expression: No

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Component #6: protein, T-complex protein 1 subunit gamma

ProteinName: T-complex protein 1 subunit gamma / Recombinant expression: No

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Component #7: protein, T-complex protein 1 subunit eta

ProteinName: T-complex protein 1 subunit eta / Recombinant expression: No

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Component #8: protein, T-complex protein 1 subunit theta

ProteinName: T-complex protein 1 subunit theta / Recombinant expression: No

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Component #9: protein, T-complex protein 1 subunit zeta

ProteinName: T-complex protein 1 subunit zeta / Recombinant expression: No

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Component #10: protein, T-complex protein 1 subunit alpha

ProteinName: T-complex protein 1 subunit alpha / Recombinant expression: No
MassTheoretical: 60.557566 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #11: protein, T-complex protein 1 subunit beta

ProteinName: T-complex protein 1 subunit beta / Recombinant expression: No
MassTheoretical: 57.276254 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #12: protein, T-complex protein 1 subunit delta

ProteinName: T-complex protein 1 subunit delta / Recombinant expression: No
MassTheoretical: 57.68241 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #13: protein, T-complex protein 1 subunit epsilon

ProteinName: T-complex protein 1 subunit epsilon / Recombinant expression: No
MassTheoretical: 61.995004 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #14: protein, T-complex protein 1 subunit gamma

ProteinName: T-complex protein 1 subunit gamma / Recombinant expression: No
MassTheoretical: 58.889094 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #15: protein, T-complex protein 1 subunit eta

ProteinName: T-complex protein 1 subunit eta / Recombinant expression: No
MassTheoretical: 59.802438 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #16: protein, T-complex protein 1 subunit theta

ProteinName: T-complex protein 1 subunit theta / Recombinant expression: No
MassTheoretical: 61.735102 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #17: protein, T-complex protein 1 subunit zeta

ProteinName: T-complex protein 1 subunit zeta / Recombinant expression: No
MassTheoretical: 59.997559 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.7 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 % / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000 X (nominal), 18000 X (calibrated) / Cs: 0.005 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 107318
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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