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- EMDB-51491: CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution. -

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Basic information

Entry
Database: EMDB / ID: EMD-51491
TitleCryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution.
Map dataSharpened CryoEM map of yeast actin
Sample
  • Complex: Polymer of actin subunits
    • Protein or peptide: Actin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsFibre / polymer / helical protein / motility / PROTEIN FIBRIL
Function / homology
Function and homology information


RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / vacuole inheritance / ascospore wall assembly / actin cortical patch / Swr1 complex / Ino80 complex / establishment of cell polarity ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / vacuole inheritance / ascospore wall assembly / 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 / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
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 cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBullough PA / Ayscough KR / Lahiri I / Tzokov SB / Stevenson SR
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Structure / Year: 2025
Title: Cryo-EM reconstruction of yeast ADP-actin filament at 2.5 Å resolution. A comparison with vertebrate F-actin.
Authors: Sarah R Stevenson / Svetomir B Tzokov / Indrajit Lahiri / Kathryn R Ayscough / Per A Bullough /
Abstract: The core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerizes into filaments (F-actin). Budding yeast possesses a single actin that shares 87%-89% ...The core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerizes into filaments (F-actin). Budding yeast possesses a single actin that shares 87%-89% sequence identity with vertebrate actin isoforms. Previous structural studies indicate very close overlap of main-chain backbones. Intriguingly, however, substitution of yeast ACT1 with vertebrate β-cytoplasmic actin severely disrupts cell function and the substitution with a skeletal muscle isoform is lethal. Here we report a 2.5 Å structure of budding yeast F-actin. Previously unresolved side-chain information allows us to highlight four main differences in the comparison of yeast and vertebrate ADP F-actins: a more open nucleotide binding pocket; a more solvent exposed C-terminus; a rearrangement of inter-subunit binding interactions in the vicinity of the D loop and changes in the hydrogen bonding network in the vicinity of histidine 73 (yeast actin) and methyl-histidine 73 (vertebrate actin).
History
DepositionSep 4, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51491.png

Downloads & links

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Map

FileDownload / File: emd_51491.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened CryoEM map of yeast actin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.0587953 - 2.6406343
Average (Standard dev.)0.00086784014 (±0.06203419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 240.192 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CryoEM half map of yeast actin

Fileemd_51491_half_map_1.map
AnnotationCryoEM half map of yeast actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map of yeast actin

Fileemd_51491_half_map_2.map
AnnotationCryoEM half map of yeast actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polymer of actin subunits

EntireName: Polymer of actin subunits
Components
  • Complex: Polymer of actin subunits
    • Protein or peptide: Actin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Polymer of actin subunits

SupramoleculeName: Polymer of actin subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 41.735547 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG ...String:
MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG FSLPHAILRI DLAGRDLTDY LMKILSERGY SFSTTAEREI VRDIKEKLCY VALDFEQEMQ TAAQSSSIEK SY ELPDGQV ITIGNERFRA PEALFHPSVL GLESAGIDQT TYNSIMKCDV DVRKELYGNI VMSGGTTMFP GIAERMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLTTFQQMW ISKQEYDESG PSIVHHKCF

UniProtKB: Actin

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 350 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8 / Details: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM Tris
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.76 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1368572
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9go5:
CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution.

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