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- EMDB-8727: The cryo-ET structure of frozen-hydrated honey bee Z-disk -

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Basic information

Entry
Database: EMDB / ID: 8727
TitleThe cryo-ET structure of frozen-hydrated honey bee Z-disk
SampleZ-disc
SourceApis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Map datafrozen-hydrated honey bee Z-disk- filtered to 60 Angstrom
Methodsubtomogram averaging, at 60 Å resolution
AuthorsTaylor KA
CitationJ. Muscle Res. Cell. Motil., 2017

J. Muscle Res. Cell. Motil., 2017 Yorodumi Papers
Structure of isolated Z-disks from honeybee flight muscle.
Mara Rusu / Zhongjun Hu / Kenneth A Taylor / John Trinick

DateDeposition: May 7, 2017 / Header (metadata) release: Jun 14, 2017 / Map release: Aug 9, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0976
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0976
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8727.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
7.6 Å/pix.
= 1459.2 Å
192 pix
7.6 Å/pix.
= 1459.2 Å
192 pix
7.6 Å/pix.
= 1459.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 7.6 Å
Density
Contour Level:0.0876 (by author), 0.0976 (movie #1):
Minimum - Maximum-0.27998948 - 0.2915187
Average (Standard dev.)-9.657E-12 (0.072596684)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
CellA=B=C: 1 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.67.67.6
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z1459.2001459.2001459.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.2800.292-0.000

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Supplemental data

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Sample components

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Entire Z-disc

EntireName: Z-disc
Details: Z-disc directly isolated from Apis mellifera (honey bee) indirect flight muscle
Number of components: 3

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Component #1: cellular-component, Z-disc

Cellular-componentName: Z-disc
Details: Z-disc directly isolated from Apis mellifera (honey bee) indirect flight muscle
Recombinant expression: No
SourceSpecies: Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Source (natural)Organelle: Z-disc / Location in cell: sarcomere / Organ or tissue: muscle

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Component #2: protein, Actin

ProteinName: Actin / Recombinant expression: No
SourceSpecies: Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Source (natural)Organ or tissue: muscle

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Component #3: protein, alpha-actinin

ProteinName: alpha-actinin / Recombinant expression: No
SourceSpecies: Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Source (natural)Organ or tissue: muscle

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Experimental details

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Sample preparation

Specimen statetissue
Sample solutionpH: 7.2
Support filmCarbon coated grids were made hydrophilic by glow discharging for 40 seconds at a high tension of 10 kV in a Cressington 208 Carbon Coater.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: After the Z-disk suspension was added to the grid it was left to settle for 10-15 seconds followed by washing with low salt buffer (25 mM HEPES, 100 mM NaCl). The washing step is crucial for the removal of salts present in the extraction buffer, ensuring that plunge frozen grids were free of contamination. Plunge freezing was carried out using Quantifoil grids (Agar Scientific) in a Vitrobot Mark IV (FEI) at 4-5 degrees C, 90-100% humidity using a blotting force of 3-5 for 4-6 seconds.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: Tilt series were recorded using the Saxton acquisition scheme (Saxton et al., 1984). Tilt angles ranged from -69.87 to +67.66 degrees starting at 0 degrees, 96 total images, with an initial step of 2 degrees. The average electron dose/micrograph was ~0.7 electrons/Angstrom2. A total of 12 tilt series, designated tomo1 - tomo12, were collected but only one proved to be useful, tomo9. The others had poor resolution due to either low intrinsic order, excessive extraction of actin or other structural Z-disk proteins, or due to excessive radiation damage.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 22500 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -69.87 - 67.66 deg.
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionDetails: Electron dose may not be accurate.

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Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionAlgorithm: EXACT BACK PROJECTION / Software: I3 / Resolution: 60 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Base on structure feature, and the fitting model, the resolution was estimated manually. Also, the FSC yielded a value of 60 A.
FSC plot (resolution assessment)

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