EMD-7116
CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state
EMD-7116
Helical reconstruction4.6 Å
Deposition: 17/11/2017Map released: 10/01/2018
Last modified: 13/03/2024
Concentration: 0.45
mg/mL
Details: 0.45 mg/mL myosin VI was added to 0.025 mg/mL actin
Details: 0.45 mg/mL myosin VI was added to 0.025 mg/mL actin
Buffer
pH: 7.5
Buffer components [9]:
Details: Buffer was filtered through 0.44 um filter and degassed.
Buffer components [9]:
| Name | Formula | Concentration | ChEBI |
|---|---|---|---|
| Potassium chloride | KCl | 50.0 mM | |
| Magnesium chloride | MgCl2 | 1.0 mM | |
| EGTA | C14H24N2O10 | 1.0 mM | |
| Imidazole | C3H4N2 | 10.0 mM | |
| Tris hydrochloride | C4H11NO3 | 2.0 mM | |
| Dithiothreitol | C4H10O2S2 | 0.5 mM | |
| Adenosine triphosphate | C10H16N5O13P3 | 200.0 mM | |
| Sodium azide | NaN3 | 0.01 % | |
| Apyrase | Apyrase | 10.0 U/mL |
Grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 298 K
Instrument: LEICA EM GP
Details: Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An additional 3 uL of myosin VI was applied. After 60 seconds, 3 uL solution was removed, and the grid was blotted for 3 seconds from the backside with filter paper..
Chamber humidity: 95%
Chamber temperature: 298 K
Instrument: LEICA EM GP
Details: Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An additional 3 uL of myosin VI was applied. After 60 seconds, 3 uL solution was removed, and the grid was blotted for 3 seconds from the backside with filter paper..
Microscope: FEI TECNAI 20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 2.0 mm
Nominal defocus: 1.5 µm - 3.0 µm
Nominal magnification: 29000.0
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 2.0 mm
Nominal defocus: 1.5 µm - 3.0 µm
Nominal magnification: 29000.0
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording
[1]
Detector model:
GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 1-24
Number of grids: 3
Number of real images: 778
Average exposure time: 0.25 s
Average electron dose per image: 1.5 e/Å2
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 1-24
Number of grids: 3
Number of real images: 778
Average exposure time: 0.25 s
Average electron dose per image: 1.5 e/Å2
Final
reconstruction
Resolution: 4.6
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 56116
Algorithm: FOURIER SPACE
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 56116
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Software
[1]
| Name | Version | Details |
|---|---|---|
| FREALIGN | 9.11 | - |
⦩ Final angle assignment
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM structure of myosin VI-actin complex, B factor sharpened to -150
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM structure of myosin VI-actin complex, B factor sharpened to -150
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 512 | 512 | 512 |
| Origin | -256 | -256 | -256 |
| Spacing | 512 | 512 | 512 |
| Voxel size | 1.27 Å | 1.27 Å | 1.27 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 6.0 | AUTHOR |