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- EMDB-41279: Yeast actin wild type -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41279
TitleYeast actin wild type
Map data
Sample
  • Complex: yeast actin A167E mutant filament
Keywordsactin filaments / cytoskeleton / cations / stiffness / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / fungal biofilm matrix / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex / Ino80 complex / establishment of cell polarity / NuA4 histone acetyltransferase complex ...cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / fungal biofilm matrix / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex / Ino80 complex / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / protein secretion / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / hydrolase activity / chromatin remodeling / DNA repair / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesSaccharomyces (fungus)
Methodhelical reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsVolkmann N / Hanein D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: yeast actin wild type
Authors: Volkmann N / Hanein D
History
DepositionJul 19, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41279.png

Downloads & links

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Map

FileDownload / File: emd_41279.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 256 pix.
= 310.528 Å		1.21 Å/pix.
x 256 pix.
= 310.528 Å		1.21 Å/pix.
x 256 pix.
= 310.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.213 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.19769605 - 0.3192549
Average (Standard dev.)0.0008068232 (±0.010466868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 310.528 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41279_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41279_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast actin A167E mutant filament

EntireName: yeast actin A167E mutant filament
Components
  • Complex: yeast actin A167E mutant filament

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Supramolecule #1: yeast actin A167E mutant filament

SupramoleculeName: yeast actin A167E mutant filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.43 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.23 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238930
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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